Can I suggest some optional options?
First one is about player relationship when he commissioned by faction, I always found silly how player relationship affect all the faction, maybe it is better to have option to keep them independent of each other? Player for example can just eradicate piracy in sector, if player have pirate commission, and player do some probe scan missions for early money, and some factions got inhospitable because they increase relation too, whole pirate faction got inhospitable too to these factions, and they start to send trade convoys there and stop doing piracy. With this option it will be less silly, since even if player got inhospitable, the rest of pirates will still being pirates. And same with other factions, its kinda strange what a single mercenary basically can affect whole faction, which have own leader and player not in charge of it, it just most silly looking with pirates )
Also speaking of pirates, how about making Corsairs and distress call ambushes non hostile to player if he actually have a commission? In the rest causes, if player even friendly but non commissioned is okay to have some hostile pirates even then, but I think it is good to give them same thing as vulture scavengers have, so even player have transponder on, it wont cause immediate hostilities since they attacked first.
Another optional option for player relationship, make locked it to faction, so like player always be hostile to faction enemies, until they got diplomatic event which causes them to be neutral, and only possible to improve relationship with factions via agents, or just leave a faction and make own one.