Toe overlap on road is common and not a big deal. If you’re nervous find some grass and ride the slowest, tightest figure 8 and circles you can until you are used to it. Throw track stands in too. Being able to stop and re-position will help.
I ride 48-50cm bikes so all my bikes have toe overlap including my cyclocross bike. You just learn to adapt. Trying pedaling figure 8s on grass and you start to get the timing down to avoid the front wheel while turning at slow speeds
I have a 56cm Trek Domane - I was in between 54 and 56 and chose 56 in part to minimize toe overlap.
I ride with my cleats as far back on my shoes as they will go, and have toe overlap. It only happens when riding very slowly (or more specifically, when turning tightly, which only happens when riding slowly) and it’s never been an issue once speeds are more than 7 or 8 mph.
I have to check at the shop, but I won’t be surprised if some of the smaller MTB’s with 29" wheels could have some TO issues. The large wheel/tire combo and steeper head tube angle on more XC oriented bikes may be close enough to cause a problem. I ride Medium or Large MTB’s and have not had an issue there. But maybe some Extra Small or Small MTB’s could have the problem. I suspect it is far less prevalent than road bikes, but could exist in a small group of MTB’s.
I have a 4” gap between my toe and wheel on a medium size Trek fuel. Toe overlap would be a much bigger problem on MTB, as it’s pretty frequent to be riding slowly on tight trails requiring tight turns.