So I was unable to re-create the issue with AI empires being given FTL tech after selecting "STL AI".

I attempted to recreate the issue with the following mods (and in the following order)

Pre-FTL Players
NSC2 Season 6
UI Overhaul Dynamic

I was able to load in a game as United Earth with 5 ai empires on a medium galaxy. I selected the STL AI start. I switched to observe, and each of the 5 empires did not have the FTL drives installed on their ships.

Are you using any of the NSC sub-mods/compatible mods with this?

Also keep in mind that advanced start AI empires will be given FTL tech regardless (if they don't get it, because they have extra planets their economy jumps off a cliff very quickly) along with Fallen Empires.

(I was also able to load the game with Pre-FTL players on the bottom of the load order, and did not try to start a game as the ship mesh in the empire selection screen wasn't loading properly, and without it you will experience a ctd. Not sure exactly why that happened but can confirm that's the issue on that side).