I ride frames that size, and every frame I've ridden gets decent amounts of overlap. It's a fact of life on smaller frames. IRO doesn't go down to 650s until their 46cm Heidi frame. As others have said, clipless helps, smaller tires too. Riding cranks smaller than 165 is dumb unless you're like 5 feet tall or less.
I really don't find it to be an issue at all, I only run into it when I'm moving my wheel around trying to trackstand on flat with my geared bike. No need to shift around so much on fixed with all that helpful back pressure, you turn the wheel away from your foot anyway.