You can also do things like get smaller tires, like 23c and get shorter toe cages and shorter crank arms to help get rid of overlap. You may want to look at comfort and efficiency though, because changing these things will change how the bike feels and how you power the bike.

With my bike (49cm Moto Track) I think just changing out the tires from 25 to 23c got rid of the overlap, although I may have changed out the toe cages by then, I don't remember. The stock cages were too long for me anyway.