I don't know where to ask this because I also don't quite understand what's going on.

"All Diplomatic Options" dosn't touch the startpos files, it just adds options to liberate faction linked in startpos to the concerned settlement.

Mixu's does change the startpos.

I'm not going to talk about Cataph or any other mods addings/replacing factions or just adding legendary lords.

Every settlements that are changed by Mixu's Legendary Lords and/or Mixu's Unlocker can't be liberated, it's the vanilla factions that are proposed.

I don't know where to look for a solution. And it can't be the load order unless I don't understand it properly, as "All Diplomatic Options" is behind Mixu's