It's easier to just install the Tint Protector kit than have to clean the molding every time you head off for a drive but I do agree that it's the sand and dust gathering in there that causes the scratching.
The fix for 2005 and on Mustangs has to be the window tint scratch felt kits though.
Without the Tint Protector kit the tint will keep scratching due to the non felted inside weather strip.