Haven't read the entire thread, just spotted it now and noticed the question: 'why'.
Maybe someone suggested it before, but my understanding of the 'why' is this:
(a) in-game: those modifications are not gene-based, and therefor not subject to geneteic engineering. E.g. the brain slugs are not some part in your DNA, they are separate organisms! While you could argue that such organisms might be cloned, that still doesn't allow you to build it into your DNA. (not sure to what extent this argument can be made for all of the modifications in question, but AFAIK most of these traits originate from outside events, they are not inherited from a parent.)
(b) out-of-game, the stacking of benenficial traits from events was never meant to happen: e. g. your pops could go psionic, or cyborg, but having the effect of both would be OP. You could argue that this stacking is required to keep up with Synth ascended empires, but that is a question of balancing and goes beyond the scope of 'why'