Pitted roof from rust under vinyl top repair

Thats some deep pitting and even phosphoric wont treat it well enough to rid it. You would be well ahead to replace the roof skin on that car.
If roof skin replacement is out of the question I would suggest media blasting the pitting and sealing it with epoxy prior to any body work. The problem with filler on a roof anywhere away from the edges is the roof expands and the filler can break free.