Most places use phosphoric acid which will leave a protective residue on the metal (most other acids will keep eating the metals if you leave them soaked in acid, phosphoric acid will not).

That being said, once you have a bare frame you can spray stuff into the frame rails as need be. I believe POR or one of those other companies has a special frame rail setup for getting into those hard to reach places.

Much easier to get everywhere when the car is stripped and on a rotisserie (Which it would be if you're stripping it like that).