ngl I kinda liked it more when the vestige ships would occasionally pop up in remmie fleets. the system of their own makes sense but, even with the bar event, it's a little ... isolated.
I can see why it'd be like that. Not sure how to give them more of a campaign presence. Maybe some Domain-Exploratorium Probe-like things you have to fight guarded by vestige or low / medium danger systems for them to spawn in.
If you want the vestige ships back you can go to EpitaphFrost\data\world\factions\remnants.faction and delete all the #s I put to comment the vestige out and that should probably get them to spawn in Remnant fleets.
Re: fixing procgen overwrite: Tried to fix it, solution didn't work, gonna need to put down some time to figure it out.
both of those ideas could be pretty neat, perhaps keeping the current system in place as like a ... high-high level, guaranteed "go here if you wanna get into a brawl" option for people seeking the ships out in larger quantities? so like say someone really wants to risk their fleet to hunt for the cool vestige weapons.