Yes the lower side of the metal is usually visible above the shingles.
Someplace I read somebody suggesting that you can bleach out water stain in a ceiling and it can save you from having to repaint. I'm skeptical if that really works, but it could be cool if it does. I never tried it. Probably takes some strong bleach solution.
Maybe you can be a guinea pig on that one.
It does seem like the flashing around that pipe is wrong. That could be the problem and you would obviously still have to get that fixed.