Oddly that's pretty much exactly what I had in mind in terms of doing it from the rear (ahem!). My biggest concern is the flipping procedure, can't envisage having the strength to do it unless it's done on the launching trolley.
I imagine the ground would support much of the weight, especially since the stern is heavier side of the boat. Balance at the top could be a greater challenge because the transom is not square.
I bought 'em from Seitech. You could probably get some foam pipe insulation at Home Depot and do the same. Or a wiggle-worm at Wally-World. I think that's basically what's underneath the fancy cloth covers.
Here's mine. I've been all up and down the east coast like this.
Note my load bars are spread out further than marginal's. My bars are about 40" apart. I purposely bought a wagon with a long roof rack so I can do this. This is probably more a personal preference than anything else. I have seen many people cartop with the load bars only a couple of feet apart.