Alright so I kind of posted this almost as a joke as to how ridiculous it was, a neat idea but something that might be added as a silly mod to games, (think Thomas the Tank Engine Deathclaws in Fallout 4)
But I've actually been thinking about it and this concept could be added to the game to influence resistance/receptivity to gene mods and TFs. For instance if you read into stuff you find that species like the Vanae and the Simii are almost immune to genetic drift and TFs; Also there are certain percent chances to how effective a TF will be, or what of your or the other sire's traits your children will have.
So; What if there was an in-game mechanic/modifier that affected the effectiveness of TFs or the likelihood of your traits being passed down to your children?
Let's call it "Stability"
Some ideas that spring to mind for related events to happen, a stable and virile male reproducing with a Myr will be more likely to produce a fertile red Myr or a Myr queen. A very stable male reproducing with a Vanae can kick of a chain where one of the two twins is born a male and you are abducted by the Vanae to explain how you have stolen the Sky Mother's gift from them. (My theory on the Vanae reproductive cycle has gotten way to deep for my own good); (Also I want a Vanae sky village and to "meet" the Vanae Matriarch, Maybe even having the offending maiden banished to travel the stars with you (She loves the Pexiga and you eventually get her functioning eyes), with the fraternal twins taken to the nursery.)
Stability could also still cause the bizarre affects when transforming between two markedly different species, probably on silly mode though; maybe even with an interesting Sera scene where you barge in demanding a refund and see her laugh for the first time.