Corrosion will probably be from trapped moisture/salts (dirt/mud) kept in contact with the frame.
Raw aluminium has to be prepared properly for paint/lacquer to stick to it (etched) so you may find going this route may not help much but if it’s going to be covered it could be fine.
Another route would be to stick some PU tape over the area then the chainstay protector over that. Or wrap something like self amalgamating silicone tape around first and then the protector for cosmetics.
PS you often get problems with lacquered aluminium frames when the lacquer gets damaged and allows water to get in between the lacquer and the frame. Lacquer/paint is porous but when well bonded to aluminium it seems a lot less of a problem for bikes than steel where you can get rust showing through paint.