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Sorry for the belated answer. I had to look into it a bit. But no I think this cuts into far too many systems in how we handle and differentiate species both in UI and game code and might just obfuscate things with different behaviors.
For some modding mechanics though it should probably be possible to get it working by creating a custom scripted_trigger that you can use instead of the normal is_same_species trigger where you check the species for different pre-defined tags. And that should help most of the scripted content at least.
 
Maybe something like this could work? <empire> is a place where you know that you execute an effect in the scope of the specific empire. <tag> should be replaced with the tag of the species whom you want to change the pops towards.
Code:
<empire> = {
    every_pop = {
        limit = {
            owner = {
                is_same_value = PREVPREV
            }
        }
        change_pop_species = <tag>
    }
}
 
Correct me if I'm wrong but the CoM / UNE situation just describes their common ancestry in the background text while CoM has it's home planet set to Unity and UNE has it's home planet set to Earth. So I don't think they are counted as the same species.
 
That explains some things. The weird part would then be that if you start a CoM game with UNE spawning from the system initializer then both of them would probably have Unity as their home planet (UNE would still have Earth as their Capital). But I guess it's something that somewhat works.
 
Yes, I've made an effect called set_species_homeworld that has the additional effect of making CoM lose their 100% homeworld habitability of Unity if you decide to set their homeworld to Earth instead. It will however take some time before this effect reaches live with a patch.
 
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