I rig my boat with a cam strap laced in the first set of bailing holes in the bow and stern for this purpose. I have never had it catch on anything and I run boney runs all summer long (North Santiam, Hood, Klickitat, Clackamas etc..).
I learned to do this from a number of outfitters on the White Salmon that do it (Wet Planet chief among them). They run hundreds of trips a year on class III-V water with low water, rocks, Sticks, Logs - you name it. If they had issues with it, it wouldn't be done any longer.
They also run additional straps in the area between thwarts that act as grab lines for when they are running Husum - these also go under the floor, but they do remove these when Husum is not being commercially run. These also don't seem to get caught on anything. I know that they DO keep them tightened down VERY tight, and they inflate their boats rock hard, this probably keeps them from having much opportunity to snag.