I think that's a good point. When you're playing around flashing ROMs it's going to get really old, really fast.

Or at least include this flag in the system backups and restore it upon switching to a new device...

If you get most/all of your apps from F-Droid, they're essentially establishing a policy of "any time you get a new phone, you can't use it for 24 hours", which is... insane?