You need to be careful about using two different metals together. There is a thing called electrolysis that takes place with dissimilar metals. Aluminum being the softer metal it will be attacked first. If you want to make a cutout to get inside that's fine. Why not use fiberglass to cover the opening when you are complete with your rust proofing. I'm referring to the fiberglass matting, not Bondo / Body filler . Fiberglass is not effected my electrolysis. It is relatively easy to work with & easy to sand if you need to shape it. You could also use the piece of metal you cut out as a filler & fiberglass it in place.
George