Was the trailer previously used for an R21? It is not a great fit, as you suspect.
Just off hand, I believe you need to at least adjust the bunks. It would be easier if you could find a marina which will sling your boat in a travel-lift and let you adjust the bunks. but it can be done if you are careful with the boat resting in place. The pressure point where you say the carpet is worn is probably more severe than it should be with what appears to be an unsupported area behind it. Whether it is damaging or not is questionable, but the fit is not as good as it should be.
It would also be better to have a roller where the bow is resting. The 2x4 is workable if the balance of the bunks are adjusted properly because the bow roller mainly supports the boat as it bounces a bit on the highway. The molding is quite beefy up there. However, a roller would be a bit more forgiving. The way we retrieve our boat, the roller is used as the first contact point and is how I make sure the boat is centered up forward. A roller would make that easier on the boat, too. (We have side rails which center the stern as the boat comes up out of the water. Those would help, too.) You should be able to find brackets and a roller to go there, if not locally then from the trailer manufacturer.