Because it represents an ever greater tragedy. The Emperor, knowing what superstition and religion could and would do tried to remove it completely and instate an empire of logic, reason, and science. He went so far as to claim he was not a god when others worshiped, humiliating one of his own sons for doing so.
And in the end, in the present, he is worshiped as a god in a rotting empire where logic and reason are often considered heresy and the likes of superstition and religion are dominant forces.
There being multiple god like figures worshiped throughout the Imperium robs that entire tragedy of meaning for me, and likely the vast majority. It works in fantasy, because as I have said before fantasy takes place on a monumentally smaller setting.
As an aside for this thread: why do you assume that female space marines are at all a good idea?
how can anyone tell who is going to be a great warrior before they turn 13?
If this is all you really take from why boys just entering puberty are the prime target for transforming into spae marines than I am afraid you miss the point entirely.
And I do believe you were told the clarification article was released four months after the release of rogue trader. Not even six months went by, gives it quite a bit of weight.