One more idea...my dealer has a guy that details the bikes when they come in on a trade (usually not a Harvard graduate, if you know what I mean). Could the detailer have washed the bike without wrapping the air cleaner with the rain sock? I could envision the detailer not knowing to do this since very few factory bikes have open air cleaners. After looking at your pics of water drops in the air cleaner, this explanation came to mind.
This, along with an overfill, is my bet. I would buy the bike, in fact I WILL trade my bike for yours strait across!!! No, not a CVO but not filled with rust and gonna blow up any minute if I have read all of this correctly. I know it would be a ton of work for me, but I love that color, so even if I end up with a Sandy damaged bike in trade, I will spend the, perhaps, thousands of dollars to bring the bike back to life. So U get a ready to ride 103 that is way faster than the 110 bike U bought if U really are that worried.
Seriously, I would use the issue to get something else from the dealer, exhaust, LED headlighting, SE Heavy breather, or something that U like.