I have Line-X, a BedRug, and a RetraxPro cover. The combination has worked out well for me. The RetraxPro does keep the water out, except for small leaks on a corner, but not enough to worry about rusting the Line-X covered bed. I have the drain tubes running out the front of the bed.
But my real reason to post was to point out a big difference between Line-X (or other aftermarket spray-on liners), and the factory spray-in liner. In the Ford video, you will note that they spray on a "primer" then the coating. With Line-X, they sand down the bed paint then apply the coating. The other video confirms this when they peel up the factory liner and the paint is like new.
I'm not an expert on this so perhaps someone can add which application is better.