So far I have had a test fitting on the new bike but haven't been able to ride it since the seat post provided was too long (won't go low enough). I can just barely straddle the bar with bike shoes on. I would estimate that there is currently somewhere 0-1/4" clearance if I stand just right. The bike currently has 23mm tires on it but I will probably switch to 25mm when these wear out to reduce the chance for flats. This will only make the stand over height worse.
I think the key is the word test, the bike builder will report the clearance issue, back to the frame builder, who, if they are good, will make some adjustments, and it will all work out....