Does the cart float?
Why does the cart not have the Trax cart wheels?
(which would seem much better for transport/portaging/etc)
In addition to what MMiller says, standard wheels should work well enough in sand with these light inflatables (remember you're also lifting a major part of the load) and are superior in all other cases (no flats, lighter, easier to insert in the water).
Is there any way to stop the cart from coming out of the holes?
Using a long bungee, hook one end on the cart, loop around the boat, then hook the other end on the cart. Alternately, loop a short bungee from the cart, through the drivewell and around a crossmember (stick or whatever, spanning the drivewell). Either should work.
I assumed that the cart should seat deep enough in the holes so that the kayak weight sits on the padded hobie crossbar on the cart. However, it does't go in that deep. Is this correct? Should I add further padding to the hobie crossbar so that the kayak weight sits on the bar?
The inflatable drivewell is a high strength, rigid and durable nylon piece. It doesn't have the issues that Polyethylene has, nor is it curved at the cart mounts, as is the Poly. I don't think you'll have any problems.
PS I'm not a Hobie engineer , so if MMiller says any different, his version is correct!