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Yah all you do is cut the hole through the bedliner like you do the bed, still looks good, doesn't make bed liner lose firmness at all, no big deal. I even put my goose-neck plate on top of the bed liner in my old truck, with the spacers it didn't even smash the bed liner.
I have the B&W turnover hitch. It is wonderful, you have the use of the whole bed. My 8 yr. old son and I put it in one afternoon approx. 2 hrs. I would suggest you put the hitch in and have the bed sprayed after. Looks real sharp.
There is no reason you can't mount the 5th wheel rails over the bed liner. They make goose neck hitches that turn into 5th whell hitches now if you use both, no matter what you do there is no deal with the bed liner.
A friend of mine has the 5er rails. He cut the bed liner to fit the rails and as a bonus they lie reasonably flat. No problems switching from 5er to Gooseneck, just pull the pins and switch 'em out.
I put the adaptor on my firth wheel and use the B & W turn over all the time. The adaptor on the Travel Trailer is a little more trouble, but I do not waste any bed space.