We just towed from Tampa to Norris Lake (730 miles one way) with our covers on. Just think about all that road grime and dirt that will get in your boat without your covers.
The "warranty" is probably claiming that they could rip or something so they won't cover it. But they aren't expensive to repair with a patch and my boat is worth too much to not tow with covers.
I used some blue painters tape on the front of the covers to keep some of the pesky snaps from unsnapping and it worked great. In addition, I also did NOT use the front rain pole. I inflated one of our tubes partially and used that instead. The wind just makes the cover look like the pole is going to poke through.
I've towed to Cumberland (800 or so miles) and Norris twice (730 miles one way) with my snap covers on and have never had a problem.