Pretty soon you'll learn to put the outside pedal "down" on turns, and it will become automatic.

My Surly Cross Check is one of the joys of my life, but once I put fenders on her, I too had fender-toe overlap just like you.

Sometimes, adding fenders to the bike just takes up some space. (I live where it rains 200+ days a year, so the fenders are worth the price of learning proper cornering technique!)