Yeah, I run into the issue of having to pay off bounties in my own territory a lot because I catch local faction bounties undermining, and (at least in Kaine's territory) those minor factions where I'm undermining are in charge of many systems, which makes it annoying.
On one hand, it seems silly and counterintuitive, and it's two game systems colliding with each other. On the other hand, I could see the local faction would view local power-aligned security, couriers, etc., as their own citizens (maybe even friends, family, etc.) living in and as part of their territory so they should be upset that you're killing these people (although that viewpoint really only works as long as power control is not considered a hostile takeover).
In the end, though, regardless of if that stance makes sense, I'd prefer gameplay accessibility to take the forefront.
Currently, I don't know if power-aligned NPCs ever actually attack you. I have never been preemptively attacked by an enemy power. Thus, I would propose that killing power-aligned ships should give you power bounties as they did in PP1. Enemy power ships should, when you have any bounty by their power, be immediately hostile. And to be clear, by that I specifically mean red-radar-blips like you're in a CZ hostile, not "they happened to scan your ship because you sat still for it to happen and found out you're an enemy" hostile.