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I would not, the trait was designed with "1 sub species only" in mind. Because of the way the Stellaris engine works, the code that gets used is "SELECT random_sub_species WHERE has_trait = gene_target"
Note the use of the word RANDOM in there - there is no way for me to control which one the engine will give me back. So if you have 2 sub species with the trait, you should expect pops to be randomly assimilated into either of them.
"How does this mod deal with sub species that technically can't be gene-modded into a diferent version?"
It totally ignores that and does let you gene mod pops into traits that you should not be able to. Adding that on would be vastly too much headache if it is even possible.
For example, the cybernetic creed has the spiritualist implants, which only the spiritualist pops of the empire can have. So if I give the spiritualist sub-species this gene-template trait, will it ignore those without the implants, or just force the gene-modding anyway?
Can I create two sub-species with the gene-template trait, so long as one of them has the spiritualist implants, an the other one doesn't?
Because this mod as standalone has too few subscribers, the 3.11 locked version is folded into Genetic Assimilation, as I suspect that what most of the subscribers are using it for anyway.
When i manage a 3.12 update this mod will continue as standalone, the folded version is just for version-locking purposes.
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=3108330591
i did find a mod that did it through edicts but it over a year with out updates and comments indcate needing a updates