We've got a Desert Fox 28KSHW with dual-electric bunk beds in the back. When fully retracted to the ceiling, we have a little over 6'-0" of clearance. I'm 6'-5" and don't have a problem at all.
When our bikes are loaded, most of the bikes are forward of the beds anyway.
The Desert Fox is an awesome rig, but it's pretty tongue-heavy...right around 1,200 lbs loaded. We're pulling it with a GMC 2500HD crew cab Duramax/Allison and wouldn't feel comfortable with a smaller truck.