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I think it's important to grant some precision concerning the question, so let's break it down a bit.

Initial Concerns: I would imagine that the main terrain on which this debate operates, at least in the first instance, is one of i) psychology and ii) intention, which I group here as they overlap considerably. i) is a concern regarding whether a person, consciously, unconsciously, or non-consciously hates, fears, or has some particular negative disposition towards trans people. And ii) is a concern regarding whether the utterer of a statement intends to voice or propagate such a view, or harm trans people. Let's break these down:
Psychology: We of course cannot be certain, without any other evidence, I think the principle of charity demands that the statement in question from Horus Heresy was not one made by a person whom we have reason to think of as a transphobic.
Intention: The principle of charity similarly demands that we don't read this statement as such, again, at least without further evidence.

Accuracy: The next issue is a matter of the accuracy of the statement, and particularly it's reflection of the biology of sex. Here I begin with a story. In 2019 I was asked to help teach a course entitled The Philosophy of Sex at the University of Sydney, an area of philosophy with which I was unfamiliar (but I needed the money). It was a great subject, and one of the most enjoyable was given by Prof. Paul Griffiths, who is an expert in the Philosophy of Biology, and has published a considerable amount of work on the biology of sexual difference. His lecture was an anomaly, as it was not one with the intention of imparting any knowledge regarding the biology of sexual difference per se, nor one aimed at engaging students in any particular philosophical issues in this area (although other courses were available). Instead, this lecture had one goal: to demonstrate how little we all know about the biology of sex. We laymen know nothing. It was a tour de force of the most complex biology I have ever encountered. The purpose was to take as a foundation that our discourse on this matter must emerge from a recognition of our own thorough ignorance of the biology of the matter, such that we do not lend baseless dogmatism to our thinking about this. A link to a popular presentation of his view is here:
https://www.appliedphil.org/sap-public-lecture-australia-a-process-theory-of-biological-sex-paul-griffiths-university-of-sydney/
To summarise his position (and I may be wrong, here, so forgive): a) there are only two sexes; b) not all individuals possess one or the other; and c) for the most part, sexual difference, from a biological perspective, is more a species-level issue than an individual-level issue.

Initial Summary: From this, I think it's fair to say that the statement in question expresses a primary-school level understanding of the biology of sex, and is properly distortionary of the reality, and it is highly unlikely that this person made this statement from transphobia, or wielded it to transphobic end. But I think that there is one more point to make.

History: Whether we like it or not, and regardless of what our own intentions and psychology may be, it is the case that language has a history. Indeed, as Wittgenstein argues, it's necessary for language to operate as language - to communicate meaning - without this. That is to say, the meaning of the words, terms, and phrases we use has significance over and above our own use. So regardless of how the phrase in question was used, or was intended to be used, and what it was intended to communicate, there is a separate issue concerning the discourse(s) with which it engages - intentionally or unintentionally. And I think that the writer of the article has a point: It may not have been made as a hateful statement, but it is one that intersects with, and strongly resonates with, hateful discourse. Discourse evolves, and maybe the pseudo-scientific transphobic discourse with which this phrase resonates only arose after this claim was published. But we cannot deny the reality that it intersects with in now, and it is a discourse which does genuine harm to trans people - a vulnerable group even in the most progressive societies; a group over which hangs the very real possibility of death in less progressive ones.

Conclusion: Given this, I would argue that we have sufficient reason to state that the statement from Horus Heresy is not transphobic, but that it should be changed, because of the harm that it does. Like it or not, we have a responsibility to counteract the efficacy of hate groups when it is within our reasonable power. And one of these needs is to be a little more careful concerning our expressions regarding the biology of sex, lest we not parrot the distortionary speech of hate-groups. This would likely not demand that GW recall all these products form those who bought them. But it would demand that they change this, and related statements in future editions of this book, and future publications.

EDIT: Furthermore, I think that we as a community of wargamers have certain responsibilities to be as inclusive as possible. This may not demand that we write to GW to demand this change. But I think it requires us being receptive to concerns that emerge from the community. And in a way that has been unfortunately lacking in this thread, which has been overly ready to speak of 'snowflakes' and 'virtue-signalling', and characterise this as a non-issue, or one over which we should pass in silence because its 'divisive'. This means saying (and remember, you don't have to say anything at all), not just "no", but rather, "I understand that we are dealing with legitimate concerns of a marginalised group, and whether I agree with this statement or not, we are an inclusive community."

Hecaton wrote:

 TonyH122 wrote:
Conclusion: Given this, I would argue that we have sufficient reason to state that the statement from Horus Heresy is not transphobic, but that it should be changed, because of the harm that it does. Like it or not, we have a responsibility to counteract the efficacy of hate groups when it is within our reasonable power. And one of these needs is to be a little more careful concerning our expressions regarding the biology of sex, lest we not parrot the distortionary speech of hate-groups. This would likely not demand that GW recall all these products form those who bought them. But it would demand that they change this, and related statements in future editions of this book, and future publications.

How is a statement made about the medical science of a fictional dystopia harming people in the real world?

Acknowledging that biologically male bodies are distinct from biologically female bodies in almost all cases in humans is not a transphobic statement, and it doesn't invalidate the central proposition of transgender people. Saying something is male in a biological context is not the same thing as saying it's a man.

Two points:
1) The fictionality of the world is entirely besides the point. Song of the South is a fiction; Birth of a Nation is a fiction. But there's a reason why they don't play on Sunday Afternoon Disney.
2) Indeed, I see little issue in suggesting 'only men can do become space marines'. But that's not the problem here. The problem was that this statement said that what it is to be a man is a matter of 'chromosomes' and 'biological makeup'. Not only are such claims false and distortionary (see the lecture I posted above), but intersect worryingly (even if not intentionally) with established modes of hate-speech.

Hence problematic. Just say "Only men can become Space Marines". There you go. Then you're not even pretending to make a biological claim.

CadianSgtBob wrote:

 TonyH122 wrote:
Conclusion: Given this, I would argue that we have sufficient reason to state that the statement from Horus Heresy is not transphobic, but that it should be changed, because of the harm that it does. Like it or not, we have a responsibility to counteract the efficacy of hate groups when it is within our reasonable power. And one of these needs is to be a little more careful concerning our expressions regarding the biology of sex, lest we not parrot the distortionary speech of hate-groups. This would likely not demand that GW recall all these products form those who bought them. But it would demand that they change this, and related statements in future editions of this book, and future publications.

But what should it be changed to? What level of strict technical accuracy and explicit mention of the edge cases in sex determination needs to be included in a context where the precise nuances of sex and genetics have nothing to do with the topic of discussion?

Something that doesn't resonate with the discourse of hate-speech. Same as the way we might speak of cultural difference without referring to people being more or less 'savage'. No-one is asking for the world here; nor even biological precision. But just be careful, if you are going to give a distortionary biological account (and, see the lecture above, it is distortionary), don't do it in a way that engages with hateful discourse. So, if anything, just be less precise: Only men can become Space Marines. Then you're not reven pretending to make a genuine statement of biology.

CadianSgtBob wrote:

 Rihgu wrote:
"Space Marines are created from human stock via Arcane Genomancy few if any understand"

That's not just changing the wording, that's changing the fundamental concept of space marines.

 TonyH122 wrote:
2) Indeed, I see little issue in suggesting 'only men can do become space marines'. But that's not the problem here. The problem was that this statement said that what it is to be a man is a matter of 'chromosomes' and 'biological makeup'. Not only are such claims false and distortionary (see the lecture I posted above), but intersect worryingly (even if not intentionally) with established modes of hate-speech.

No it didn't. Read the actual quote:

“The process by which Space Marines are created relies inherently on the hormonal and biological make-up of the human male, meaning that only males can be subjected to the transformation.”

The quote very clearly uses the word "male", not "man". And nowhere does it say that all men must be male with XY chromosomes and male-typical phenotypes.

Something that doesn't resonate with the discourse of hate-speech.

We already have this. None of that in any way resonates with hate speech. You have to really reach to find the slightest superficial connection to a particular form of hate speech and then build that superficial connection into layers of meaning that are simply not found in the GW quote.

My response:
1) 'Male' vs 'man' seems to me like a distinction without a difference. A man is male, a male is a man. The question is what constitutes 'maleness' or 'man-ness'. And that is exactly what the sentence goes on to specify. And so my next point:
2) As mentioned in the article, the discussion of 'hormones' and 'biological make-up' very much is the language used by transphobes in relation to what constitutes male/man. And it's just factually inaccurate (see linked lecture). Hence the issue.