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Honestly, while this mod does make Improved Genetics more realistic, I think it also kind of swings the pendulum slightly in the other direction, making it unrealistically a bit too easy to "breed" genius, attractive, etc. family lines that don't experience any drawbacks from consistent inbreeding. The problem is just that there aren't really enough negative recessive traits in the game, and there also aren't any recessive positive traits or dominant negative traits.
If you started the game with the mod, though, or if you're still getting the trait on characters whose parents didn't have the trait, then it's probably a mod conflict. In that case, if you send me a zip of all your mods, I could sort through them and find the conflict, and potentially add them as dependencies to fix the conflict. You could send that through a google drive, mediafire, or dropbox link, or email me at quinstudios@gmail.com.
That said, if you want to add back the inbred trait, it shouldn't be hard. This mod only edits one file (if I remember correctly), and it's pretty self explanatory what each line in the file does, so you could easily just remove that line.
For example, if using this with, say, Improved Genetics Advanced, then the more you inbreed the more likely you'll increase recessive genes like dwarfism, harelip, lisp, ugly, clubfooted, imbecile, etc.
The main purpose of the mod is to make the mechanics of inbreeding a bit more accurate to real life (when used with one of the mentioned mods). Inbreeding irl doesn't magically make offspring mutated or lunatics, unlike its portrayal by popular media. All it does is increase the chance of passing on and expressing recessive genes that are already within the family's gene pool. This means that it's perfectly possible, while likely very rare, that if you happen to have extremely healthy genes and very few negative recessive genes, inbreeding may not actually have any negative effects.
Ultimately, I see it as a tool. The way it's used is entirely on the user. For my part, I definitely wouldn't ever use it to completely disable incest penalties, but of course I'm sure plenty of people downloading it will. It's kind of just a trade-off that I have to accept.