If you can get the hitch to fit "as is", you should be fine and the hitch will wear through the liner pretty quick. If not, go ahead and grind or sand the liner out where the hitch mounts and just go on. They should not have put the liner on over the rails but the only way to repair that bit of stupidity is to remove the old rails, re-spray and then install new rails. The chances of them doing that are slim and the fight to MAKE them do it probably isn't worth it. Best shot here (to my way of thinking); correct it yourself and make sure EVERYONE knows that Rhino Liner is NOT the way to go. Just an old man's 2-cents.
Happy Camping!