I suppose. I've personally been trailering cats for about two decades and never had any significant issues with stuff getting kicked up from the tow vehicle. If it's a concern, get a set of mud flaps, and if it's a major concern, get some hull covers. Both of those options still seem a lot more convenient than having to lift the boat up an extra foot to foot and a half each time and not being able to get into your trailer box. Heck, if you want the boat higher off the ground, weld up some extensions to raise the trailer crossbars up an extra foot. Incorporating the crossbars into the box just makes no sense to me - I don't see any real compelling reason to build a trailer that way.

sm