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.