I made a custom United Empires faction. I just wanted to change a couple things, namely give them culturalists at every rank and give my populations the +FIDSI per pop. on planet. It was great and I had a ton of fun. But, when I got to the empire quest that makes you choose to stay as the United Empire, Mezari, or Sherydyn I choose to stay as United Empire thinking it would keep my custom options. All my pops had their icon changed to the original imperials icon and their bonus was only +1 Influence. I was a little dissapointed. I liked my custom United Empire and wanted to keep playing it, and there was no option in the game to do so unless I want to try and ignore the quest completely which is unreasonable considering it involves things that I want to accomplish anyway. 

I really think the questline for the Empire shouldn't change a custom faction back to vanilla empire if a player picks the "stay as United Empire" quest option. 

Edit: I realized too late that I posted this on the wrong game. I'm not sure how to delete it.