I think you're overthinking this. Lol. First you said you're not worried about appearance, just rust prevention, but then you're calling body shops getting expensive quotes on full repairs. If you're really only interested in rust prevention, which it doesn't appear to have started with any yet, do what others have said and use some touch-up paint on the colored surface and don't worry about the aluminum channel trim. It will not rust. Although, it would look much better with a dab of black paint over it.
If you're worried about appearance, have it repaired correctly.
The estimates were simply for a ball park. If it were plenty cheap, then I'd get it done fully. But yeah, I'm totally happy with a tiny little knick, as long as it doesn't rust. That's all. Right now the plan is to do some rust converter just in case, prime, then paint. The primer is black, so I will put that on the aluminum as well and see how it looks. Otherwise I have some other black paints that I can play with until one looks alright.
