Cool, if you're pretty new to it that might just be the case. I do wonder how much I move my feet about without thinking..I've tried a few different positions but I think I'm just not used to having the same consistent foot placement with flat pedals, or maybe I'm used to shifting foot position on the fly, often without conscious though.
Slightly related, I have size 12 feet and certain cleat positions make toe overlap much worse. I didn't use to experience toe overlap, probably as it was easier to just shift my foot temporarily.
Minor rant: why don't the bigger frames have a longer wheelbase?? It's silly having the damn wheel so close to your feet
I'd have thought it unlikely that you're subconsciously pre-empting a toe strike - more likely you want the cleats a bit further forward to get the same position as you prevously had with normal shoes... although of course there are other factors - pedal stack height, toe length of shoe etc.
Bigger frames should have longer top tubes / more reach which should mitigate overlap issues; indeed it's usually small frames that suffer the most in this regard as the wheel size is usually fixed across the whole range so proportionally larger on small frames.
It's potentially not just a size thing, but also body proportion. You'll be more likely to suffer from overlap if your legs (especially femurs) are longer than average, or you feet larger than average..