Oh - duh - I did a TL-DR on the opening post, and didn't realize the rack and fender are part of the OEM build/ship. For whatever reason, the online photos of the bike show the rack and fenders attached in a variety of ways. Best quality pic I could find, however, indicates that yours is not stacked right:
Looks like the rack should go right to the frame eyelet, with the plastic extension stacked outboard of it. Then the plastic extension should point directly aft, then the fender stay attaches to the aft end of the extension.
Yes, those fenders are snug, even in all the stock online pics available. One argument is that more space between the tire and fender means more space for road crud to get past them.