I had the aluminum frames on my Hatteras painted when the rest of the boat was painted; if the painters are skilled at painting aluminum, they will come out well. Mine were painted with aluminum colored Imron and clear coated. So far, so good. I agree, though, that if it is not done right, there will be problems, and quickly. I did use stainless screws and they have not been a problem, but the potential is there. (no pun intended) I believe that originally Hatteras may have used Monel screws, which may be less galvanically active versus aluminum than stainless. Monel screws are still available from Sam's, but they are quite a lot more expensive than stainless- 3X as much, I think.
I would not put the windows in with 5200. If broken, they will be hell to remove. It is not a load-bearing assembly. If I were to remount the window frame, I would use 4200 or something similar. That way, if they ever have to come out, it will be doable without major destruction. I would not rely on AntiBond to get frames out that were caulked in with 5200, no matter how good AntiBond is supposed to be.
Finally, if the frames were anodized and then painted, the anodizing is probably still there under the primer. Unless it was ground off to prep the frames when they were painted.
Which boat? I'll look if you want. I'm in your area.