Oh yeah... I did try Ganondorf and Zelda there first while trying to figure out relevant locations for each character (also tried Kakariko for Sheik), but there wasn't any difference, so I didn't bother checking the rest before heading to the Bridge of Eldin.
Okay, so I've tried this out for myself now, and sure enough, when I scanned my TP Link amiibo on the Bridge of Eldin, I did get an exclusive item almost every time.
However, while I was there I thought I'd try my other amiibo... Toon Zelda, Sheik and Ganondorf showed no noticeable change to...
Could just be that it's only OoT Link that works with the ToT... MM Link would probably need to be used in locations that reference Majora's Mask... e.g. Romani Plains.