Yeah they will turn on each other due to the simplified faction system. Making any changes to that behavior in the wider more complex environment could be dangerous and lead to lots of serious or difficult to predict bugs, so it's not going to happen unless there is a larger review of faction relations, which is
also not going to happen for the same reason
Basically Cogmind got a lot larger than originally planned for, with a much larger web of connections, so the initial systems didn't anticipate these needs and ended up just being used as best possible without adding too much internal complexity. You will find a number of similar things throughout the game.
I did recently introduce a new separate group of more "variable" factions specifically in order to handle the very complex possible web of relations that can occur in the Recycling UFD scrap lab event between some NPCs, and I imagined going back and making other such changes throughout the game, but it's just a ridiculous amount of work for little relative gain, so all of these things will remain as is. Going forward I will be able to make use of these where necessary, which is nice...