Re: "With the F-35 I'd imagine the flight control system masks any issues from the pilot."
'Except the reports seem to be saying the handling turns to s**t around this range.'
I haven't read the report although I recall it being a bit of an issue a few years back, however when the say the handling is degraded in the transonic region that may be from an engineers point of view, where it is but that doesn't prevent it being masked from the pilot. In the F-35 you move the controls and the aircraft figures out how to do what you've asked, there's no fighting with the stick to make the aircraft behave if you don't move it the flight control software will do its utmost to keep you pointing in the same direction.
Incidentally avoiding prolonged flight in the transonic region isn't a bad idea as drag reaches a peak before you become fully supersonic at around M1.2.