Toe Clip Overlap is OK on a competition race bike but on a commuter bike it can cause problems, eg when doing a track stand at a junction, or low-speed manouvering.
TCO is a design flaw and is not neccessary. Some manufacturers accidently build in TCO, esp when they have to buy in their forks in a limited number of geometries (ie trail). Long cranks and large toe clips can also contribute to TCO.
The pedal to wheel clearance factor is not generally published. You have to check out the bike yourself.