I haven't noticed anything on mine yet but keep in mind its a weekender and parked in the garage when not in use. I have no idea how cars are painted on an assembly line but what it looks like to me is that the paint didn't stick to the primer, so if they did wet on wet, those spots could have dried and the paint didn't have anything to stick to ( high doubt that they wait for the primer to dry and then sand every car before paint) also i wonder if the lack of clear coat or thin clear coat has something to do with it as well. Mine appears to have no clear coat on the engine bay edges like yours as well.
I don't have any body work experience how ever i did work in a collision shop for 5 years and worked close with a few good body men so i will pass what i know along.
Metallic is a pain to spray to get it to match with that being said it can be done. Lots of things effect that, temp, gun pressure, distance, how fast, proper mix etc. Also it depends on where you are spraying, under hood you should get away with hard lining to the edge of the fender where it meets the hood and just doing a blow in and no one should notice too much. The door area might be a different story can be seen a little more so it harder to blend.
However it is possible to get a very good match, I had all my body kit pieces painted, tunnel cover and a bed side done as well, I'm not to good with colour but i cant tell the difference on what is factory and what was painted and i'm happy with the way it turned out. The fellow who did the painting actually said it was an almost perfect match. He also knew I wanted the colour perfect and took the time to get it that way. I also weighed and mix the paint my self to make sure of no short cuts.
Up to you really if you want to do a blow in or paint the whole thing, if there is a bunch of marks and dings everywhere why not give her a freshen up to have her looking like new again and that way the paint and clear would be seamless! I do have the paint mix sheet for mine and if you want shoot me a text or a pm and i will send it to you as we share the same paint code.