The commission fixes so many problems! As a bounty hunter, you don't suddenly get stuck without targets for a few months (well, you still get stuck without named bounties, but at least there's something to tide things over). And when you do happen to get a system bounty from your allowed faction, the bonuses stack, which is excellent. The greater ship availability in the black market is also extremely nice.
I allied with the Hegemony and they immediately declared war on everyone but the independent (who themselves declared war with the Tri-Tach). Needless to say, the sector is a lot more of a dangerous place.
So far I haven't declared war officially on either Sindria or the Ludd, so each month I get whacked by the 10 rep penalty, but I still hunt those factions with my transponder off. I can make up the 10 rep easily enough if I'm actively hunting trade fleets, and if need be I can turn the transponder on, take a little rep hit, and fly away from the enemy murder fleets (not to mention still trade with them). The Hegemony may not like my devious ways, but they'll still pay good bounty for whacking their enemies.
Also: I finally used terrain to shake an enemy fleet. I'm kind of ashamed that its taken me this long.