That has to be the dumbest thing to remove from iTunes when you a bunch of Electronic/Dance music CDs mixed Gapless. Now I am seriously annoyed by this changes, or am I not seeing it anywhere.
I had an album that was gapless. It got scratched and wouldn't play, but luckily my CD RW drive could read it, so I made a copy. After that the original died, and nothing would see it.
It was some years later, when I ripped it into Itunes that I discovered the copy process had put a 3 second gap between the tracks.
I just edited the tracks to remove the silence, and the album was gapless again. I didn't even know there was a gapless setting in iTunes at the time.
I suspect that modifying the start and end times of a track in iTunes would give similar results.