The 5.5-foot box is the smallest available on a Ford full-size pickup, but carrying capacity isn't really what the Raptor is all about. As long as you can get a dirt bike back there, you're good to go. You will have to wedge it in diagonally, however. It is of course possible to carry bikes with the tailgate down.
Drivers who are heading off-road will appreciate the Raptors more compact rear end — it makes the truck easier to sling around when the pavement ends.