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So the new Inquisitor codex has an allies matrix in which Imperial Guard are 'Battle Brothers' and Chaos Space Marines are 'Come the Apocalypse'.

Does this mean I can take IG as my primary and ally with both chaos and inquisitor allies.

The BRB doesn't really cover multiple allies but here are the relevant sections as I can determine:
BRB 113 :
"Find the row for the codex of your primary detatchment on the left side of the matrix. Then find the column for the codex of your potential allies at the top of the matrix. You'll find the level of alliance at the intersection of the row and the column" (this supports the case that you can ally as described)

The battle brothers entry refers to "two or more armies" but doesn't give any context and it is a passing remark (presumably to do with double force org?).

The levels of alliance section describes how units treat one another (can target will psychic powers, treat each other as enemies etc) so without applying a 3 way permission matrix it would be unclear how the chaos and inquisitor units would treat each other. (this undermines the case that you can ally as described).

I am open to either interpretation. I mostly want to add some traitor inquisitors to my traitor guard but if this is not possible I will just use the CSM codex and have the chaos counts as.

I see an issue with it rule wise, the Inquisition book just tells you to treat the inquisitors as two seperate sets of alliances. One with IG (Battle Brothers, so thats fine) and one with Chaos (CtA), that one isn't allowed, so I guess technically you can't do it.

Aw that's a shame, guess I will have to go guard only or guard and marines. At least till traitor guard get a book.

I personally see no problems with this.

Seeing that its not the Inquisitor AND the CSM that allies together but the IG AND he Inquisitor who have a special separate ruling.

Like Allies and Fortifications have their own slots, Inquisition has his own Ally slot.

So compulsory HQ #1 inquisitor, HQ #2 IG dude and 2 or 3 [/i]%6 units and CSM as allies.

And that boys and girls is how you get Radical inquisitors back in the game

no its not slayer,

the INQ codex literally says you treat it
as
A is allied with B and C, three sets of allies,

one cannot have three allies, and claim that "only these two are allied, and these two"

from the codex

Note that the Inquisitorial detachment may have a different relationship to the models from an army’s primary detachment, and the models that make up that army’s ‘regular’ allied detachment (assuming there are any). For example, if an Inquisitor was part of an army where the primary detachment were Imperial Guard and the allied detachment were from the Tau Empire, then the Inquisition would treat the Guard as Battle Brothers, and the Tau as Desperate Allies.

so in this case, you would treat the IG as BB, and the chaos as "come the apocalypse" IE cant do it...

as much as i WANT you to be able to BOOOOOO

Oh i see if for once they explicitly wrote it, then yes it seems there is no way around it.