I know this seems a bit of an ambitious suggestion, especially after having just finished the compartmentalization of all of the Modular mods, but what about having a territory boundary beyond planet gravity determining spawn types/factions.
This seems possible if working in conjunction with thorwin99 utilizing the progress he's made with worldgen2.0. There is already a star system designer that establishes spawn regions for procedural elements. Now, those are apples and crayons, but the infrastructure might be there to enable making system boundaries for certain factions as those introduced in either one of your mods, or other MES mods. This could be a neat way of stepping away from PCU determining the severity of the spawns, but instead into the more natural wrong place, wrong time scenario. If you knew a hostile faction owned a particular section of space and/or planet, you might be forced to otherwise route around them if your combat abilities aren't up to snuff. It could add a whole different dynamic to the game, one that gets even more interesting with aienabled jammed in there. Naturally, Reavers would stalk every corner without boundary.