In the 2nd photo, it looks as though there's what's called an "open blend" in the sail panel (C-pillar). It may be possible to polish that back so any further repair can avoid re-shooting the roof; if not, should be able to backtape that contour.
The flaking on the quarter could be from a lacquer primer and/or paint that began cracking and over time allowed moisture intrusion.
Repair will involve expanding that area to clean it up, but at least you have good contours for back-taping.
Check around at local paint suppliers to see if there's a painter in your area who's skilled at solving these types of problems; it also requires an enthusiasm for the task.