Look at the surfaces of non-painted bolts and caps, they are hot zinc or something but just look how they have been stained, it looks that some chemical action has been going on. Anyway, this does not mean that a good paint job should have came off like this. Double-anyway, I don't think things like that need to be fixed on an out-of-warranty Versys 650. This is not your BMW R Nine T or Ducati Scrambler Cafe Racer, it is not meant to be all shiny show off piece. Just clean it with WD-40, let it have and develop its natural patina over time and enjoy keeping it technically in good working order. Any dollar you would spend on fixing paint and scratches is better spent on tires, chains, cables, etc. Anyone looking at the bike from more than a foot distance does not see any of that petty sh#t, all they see is if you are enjoying your bike and riding it around or sitting home touching up some annoying paint.