When I first started riding a track bike, it was my first experience of ever having toe overlap and it totally freaked me out. I was really worried about it. Despondent even. Then people started telling me I would just get used to it. And I did. Your brain and body just eventually "know" sort of automatically what movements you can't make (i.e. where in the pedal rotation it's bad to make a sharp turn). Obviously, in an emergency situation, this phenomenon is uncontrolable, and I guess a little dangerous. But track bikes weren't designed with "sharp turns at slow speeds" in mind. Tis' the price you pay for being on the shorter side and riding em' in the street.

FYIW, when I made the switch to clipless from cages, the toe overlap vanished.