Would think it would be combination of protective/seal and type of metal would give the best protection from corrosion/rust.Yes, I was very intrigued by the side trim delete with the Tacoma upper molding. In the end, I think that will wait until I'm ready for a repaint (if ever). I should be good for quite a few years now. But @highkick05 definitely insist on having the new glass and trim installed properly if you're going to all this effort. If the holes aren't already oversized, they should use the factory rivets. If they've been drilled out, I'd see if you can find some larger plastic coated rivets. I just don't see how you'd get a self tapping screw in without scraping off whatever edge of the hole is prepped and primed with, and there's the beginnings of the rust again.
Guy I talked to seemed to think the installers know what they are doing, and did bring up the point of holes being drilled out for the screws.
I'll give the sprayer a heads up and trust that it gets done well.