It seems to me that if you're going slow enough to have toe-overlap issues (since they only really occur at low speeds), dooring won't be an issue since you can just stop in time to avoid being hit.
I do have a little bit of toe overlap with both of my bikes, and I've sort of gotten used to it. When I know that my foot might hit my wheel (or fender) I can angle my foot a little differently, and straighten out the wheel just a teeny bit for the brief interval until I've cleared the wheel. It only takes very slight adjustments, so it doesn't reduce my maneuverability all that much either (though I suppose the severity of the toe overlap would make a difference).
This was something I didn't consciously set out to try to learn; I just sort of eventually adapted to my toe overlap.