if it were a mountain bike or cyclocross bike... you need clearance... However, for a road bike, you can get away without much or any clearance... As long as you're comfortable with it.

You're going to tilt the bike slightly everytime you dismount anyways...

If you check the rivendell website, they basically determine standover height as distance to pubic bone, and ignore all the soft tissues...

I don't have much clearance on my road bikes and have no problems with it - because slightly larger frames fit my body better geometry wise than smaller ones do.