The player's commissioning faction sending expeditions against the player is going away in 0.9.1, at least.
Yeah - this is a good change.
Still - getting raided by a faction who has an actual trade convoy in my system at the same time as their raiding fleet is profoundly jarring.
I don't mind the raids at all. They absolutely need to exist - but the lore needs work.
I'm totally cool with Hedgemony sending "mercenary" fleets who are not flying their flag to raid me while they are busy pretending to be my friend while wishing I were dead.
It's the "Were friends, but I'm going to stab you in the back and get angry with you if you defend yourself!" that I find irritating.
Treat the raiders as an invasion fleet either with an association but no penalties, or no association. Or let the raiding fleets grant me a "casus belli" for 30 days or something to retaliate via a raid without a standing loss.
Finally in the late game the AI just keeps sending their hopelessly outmatched fleets into the meatgrinder with no real purpose.