The fact that you get merits for just rocking up and shooting settlement guards in the face is going to definitely add some BGS effects.I was wondering what effect the powers would have on PMFs and the BGS in general, but so far it seems like there is no direct connection, though I suspect that there will be some potential accidental side effects.
(it'd be nice if the merits were weighted towards the amount of control the faction has in the system, otherwise I expect people will just hand settlements to a sacrificial lamb at 1% inf in order to not get their bgs messed with that way)