A very good question i think.
Unless you have the rarest of rare custom covers with a slew of bungees fitted just right, I would not even think about covering it in transit. All the professional guidelines dictate transporting your boat completely uncovered. With or without special liners to protect the gel, a cover will likely do exactly what you fear: abrade the gel.
There's really little need to worry about a Donzi in transit. Give it a healthy waxing before you go. Maybe even wait on some of the buffing until you reach your destination if you are worried about pebbles and such hitting it on the road. Stow the upholstery in the bow, dry, and take her for a ride. Save your money and put it towards a great custom cover. If it rains, so be it.
I know of a couple of folks (Dr. Dan, Undertaker) who seemed to have covers so tight and fitted that they managed to be okay at highway speed, somehow. Meaning they were immobilized and the covers apparently don't sand the gel. You'll never get that from a cheap off-the-rack cover.
"I don't have time to get into it, but he went through a lot." -Pulp Fiction