Trying to figure out how to setup True PVE along side this.  

Does Raidable Bases simply override the functionality True PVE uses?  For example, if I have the flag TurretsIgnorePlayers, will pasted bases by Raidble Bases have non-functional auto turrets?  

I'm trying to prevent turrets on player bases from hurting other players.  While at the same time having turrets from Raidable Bases still work as intended.  Ideally, Sam Site too.

Same for Traps.  Will Raidable Bases override the True PVE flag "TrapsIgnorePlayers"?  So that bases from Raidable Bases with shotgun traps still work against players?

ya, Raidable Bases will override TruePVE. TrapsIgnorePlayers and TurretsIgnorePlayers will not work at raidable bases. Raidable Bases plugin controls that and overrides what TruePVE would normally do.