The parts you should have the body shop remove are the front windshield and rear window. This way there’s no paint lines next to the molding going around the window. A good body shop will require the windows to be removed as part of the warranty that you’re given.
Sanding the car down to bare metal is nice, but not required. Good body shops now use a chemical stripper that eats the paint right off of the car, but leaves the undercoating. The only parts that would need to be sanded to bare metal are the hood, roof, and trunk.
These are the panels that are most likely to peel later on, and if you get a warranty that covers this the body shop will do everything they can so that it won’t peel.