Its the kind of thing that freaks you right out at first, then as you get used to the bike it becomes a complete non-issue.
Two of my frames have had this, a paddy wagon and an old tourer. Both had HUGE overlap, one I discovered on my first spin in the carpark behind my flat, spinning the bike around I caught my foot and went straight down onto the deck. On the tourer I discovered it while weaving through traffic, though managed to stay on as the bike stalled.
Thereon, I never managed to trap my foot again on either machine. You do have to think about it making slow tight turns, but I found it a fairly intuitive technique swap and it was never an issue again really.