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My go to explanation for the 11th (purged) primarch is that he was able to procreate and (by extension) so too were the space marines in his legion. Consider the extreme danger it would pose to the imperium if there was an entire family of primarchs and a self-sustaining and growing population of loyal marines.

Alternatively, less radical, the 11th ended up on a planet that existed within a human/xenos Startrek Federation type empire. He was raised believing in equality of the the species and cooperation. So, when the emperor stumbled upon him, he could not let such an example survive that would potentially undermine the loyalty and devotion of his fellow primarchs, the legions, the masses of regular humans, etc.

In my head it is that the genetic mutations of the two lost legions and their primarchs were so flawed that they became too much of a problem. Their very nature suggested flaws in the emperors design worse than those in the other legions and so they were purged. Perhaps something that occurred in the Rangdan Xenocides pushed the aberrant genes over the edge.