I could so the same for hostile contacts - splitting into controlled and non-controlled systems and making the former non-interrupt. However, that could lead to players accidentally not intervening when one of their ships is in a hostile system. They would have to remove the control flag before entering so they got the interrupts. I imagine that could cause a lot of problems.
I could see it working if it excluded the alien systems where player ships/populations were present and the systems adjacent to those systems (if the player is able to detect an incoming jump incursion, he should certainly be notified). That being said, this sounds like a very unwieldy setting, and personally, I wouldn't use it for fear of missing something important. I think it would be far more beneficial to identify and eliminate root causes of NPR ships getting stuck to rid the player of inconsequential interrupts in the first place.
Also, since we're vaguely on the topic of buoys, I recall you saying you added a POI for buoys detected by a NPR, but it's not in the changelog. Could you please elaborate on how that would work? Am I correct in assuming that a buoy detected by a fleet operating under "Investigate POI" orders will be targeted immediately, but a buoy detected by an escorted non-combat group will not cause it to approach and will instead require another operational group to come take care of it?