Probably (maybe?) some of the hardware - tuners and pickups.
It always used to be where they're made didn't it. I can't imagine they have multiple factories spitting out CNC bodies and necks to different standards around the world, so nowadays it's probably just where they're finally assembled.
Well Squier is generally Far East. China for the Bullet/Affinity stuff, Indonesia for Classic Vibe etc.
The Mexico plant does things very similarly to the American factory I believe. So they do some initial CNC on the neck and then hand shape them. Not sure what they do in the Asian factories.
what is the material difference between squier / fender instruments these days? is literally just a sticker?