On the paint, don't know. Probably.
On the panels, heck no! That stuff looks good! All you have are holes where the spot welds were drilled out. The rule of thumb is to keep rot-free metal. Holes can be filled. Rot has to be cut out.
On the fenderwell, you can mig up the holes if you like, you can cut a new flange and weld it on, or you can plug weld those holes to the new quarter skin. That latter is tough because of space...I know. I would make sure that there is enough metal on that lip for your welds on the quarter and go with it. When done, make sure that you thoroughly prime the area and if you are doing undercoating, get that coating on the topside of that lip to fill in any remaining holes.