To be clear, there are areas where the player would not have to fear patrols hounding them for having the transponder off, right?
If I have my transponder off well outside of Hegemony territory, into pirate territory, and some lone Hegemony patrol/pirate hunters just happen to pass by, will they take interest? Will they understand I just wanted to slip past pirates? Is it an instant rep hit in all situations, or is there context in terms of whether I'm in that patrols' system or otherwise under their authority?
You don't have to worry about independent or "free port" patrols giving you trouble.
Patrols don't stray outside their system (aside from a small area around it in hyperspace), so any time you meet them you're in their jurisdiction, so to speak. Potential "war fleets" and such probably wouldn't bother you about the transponder, though, but they don't currently exist.
Maybe no rep hit when you have a very good relationship with the Hegemoney or the patrol commander?
Maybe the latter, but doesn't make sense unless those persist for longer than one patrol. Which they probably will eventually, but. The former, I don't really like - you're cutting out the "transponder off" downside entirely, and it's all upside from there on out.
