I did cover the most vulnerable tubes with helicopter tape before, just to have a reasonable attempt at avoiding scratches. I went naked because of previously-reported cases that if you have something visible they might handle it with a bit more due care than a generic-looking canvas bag. I got some quite serious frame damage last time when I packed it as well as I could in a bag with lots of padding. Still can't figure out how they managed that. And of course, after using it very often, almost daily for well over a year, it has become much more of a utility item than an objet-d'art. So I am no longer super-fussy about it.

The bent thumb-screws are obvious with hindsight - they do stick out quite far. Still, the bike must have been banged down on those. I am speculating it was stood up on them in the aircraft.