I was looking at the same sorts of things that Cookiemonster364 was, and found a few other places where "NOT { is_same_species = owner }" returns incorrect results with the changes from 1.2. One of the places this construction is used howeveris in "playablerobotsupgrades.txt".

This is kind of a large file, but it seems to do all of its work in options similar to the one normally triggered at game start. These events don't display windows, so I have to ask, do these trigger in any way at all? An event in playablerobots.txt handles granting the appropriate traits when you research the appropriate technologies, and I think the name changes are also handled elsewhere. Does "playablerobotsupgrades.txt" do anything? I'd like to be sure before I go messing with it.