Spoke to my tower controller today. He reckons a runway incursion is only at surface level and only when ATC / SMC is active. My airport turns to CTAF at night during which it's pretty much all at pilot discretion. However, I was airborne in the vicinity of 2 incidents recently in CTAF hours which prompted my questions - one of which actually caused the tower to urgently open 15 minutes early to stop a situation that they were watching develop, (because they actually start watching about half an hour before opening) and another which was much less of a concern, but a concern nevertheless. Luckily, I was able to talk over both situations with him, and also he was in the tower on both occasions and knew exactly what I was talking about. He gave me their viewpoint on it and I gave him mine, and it was a valuable discussion in terms of clarifications for both of us, and we both determined that there are some things we should probably read again. He also told me that a runway's vertical clearance does not have a finite limit but goes as high as is necessary for safe separation between aircraft. Go-Arounds could necessitate higher runway vertical limits than touchdowns. Helicopters often cross runways at low altitudes while aircraft are maneuvering but risks and clearances are constantly and fluidly monitored. I found that the discussion left me with a high appreciation for what ATC are doing, and also helped to establish mutual respect as opposed the frequent mutual animosity that I see in many pilots.
I would encourage others to find their towers number and call them (during quiet times) after any concerning incidents to make sure all aspect of any situations are known, and to discuss how anyone's performance or professionalism could be improved. It should serve to ease any tensions in sane people.