It's a very common design fault, especially prevalent in American designs, where they take no account of mudguards even when the fork has provision to fit them. Some bikes even have toe overlap with a bare tyre!
If you want to avoid this fault - and you should - you will need to restrict your choice to British designs or go custom, strictly specifying the minimum front centres dimension. Amongst ready-made bikes of the sort you are after, Thorn Audax is one of the few that should give the necessary clearance.
Edit: In reply to pigman, toe overlap does occasionally cause riders to fall, never at high speed, but it is possible to fall into the path of a faster following vehicle whilst riding slowly. I've known (sometimes seen) riders fall due to this fault when starting off, zig-zagging up a steep hill, weaving through a traffic jam and negotiating cyclepath obstacles. Toe overlap with a front mudguard can be even more dangerous. It damages the mudguard and encourages the rider to adjust the guard very close to the tyre, so it becomes liable to jam if a stone is picked up. Riders have died or become paralysed as the result of a jammed mudguard.
I find no correlation between bikes that handle well and those with short front centres. In fact I prefer the front wheel a bit further ahead for another reason too: it allows harder braking without risk of pitchover, so I'm happy riding faster downhill on a bike with long front centres.
The only problem with longer front centres is the availability of shorter stems to go with the longer top tubes, and longer rake forks to go with the shallower head angles. If these components can be sourced the riding position and handling will be just as good, if they can't it will be compromised.
Unfortunately there's a hair shirt tendency amonst sporting cyclists that tends to construct a performance myth around any factor that makes their bike somehow more exclusive. Toe overlap does this perfectly: no trouble for an experienced racer at speed, but slow novices fall off. Very funny.
Anyhow: the norms of racing frame design have evolved with scant regard for toe clearance, with the result that we have standard designs of fork and a limited choice in stems that makes it a bit hard to design a good bike that has it. Hard but not impossible. Some manufacturers meet that challenge, most do not.
I see it as part of my job to stimulate a demand for bikes that not only perform but are also safe against easily forseeable dangers.
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Chris Juden