For the most part, when TC was in the cockpit, it was in the NAWDC jet painted up for the shoot with all the cameras installed. Not sure the extent to which he flew in 122, but they also shot a bunch of stuff in Whidbey (with the NAWDC jet).
He also had a habit of trying to goad the actual pilots into doing unbriefed/dangerous stuff. Kind of a dick move, IMO. CNAF already waivered a bunch of stuff to let them get some really cool shots.
Is there any data on whether or not he did get to fly at the boat? He “claims” all the flying scenes are real and we see him on the catapult in the trailer.