I have the B&W Turnover Ball and Companion FW hitch; love 'em both and use them both regularly. If your truck has the OEM underbed hitch, I'm surprised that it would stick up that far, as the whole purpose of them is to be able to leave a "clean" bed. My TO Ball base sticks up not quite to the same height as the top of the corrugations in the floor. The 2 u-bolts for the GN safety chains do stick up slightly higher than the corrugation, but that's really not an issue. A Correct Track suspension mod will give you about 2" lift. Need to be sure that the springs are in the lowest holes of the hangars; if not, move them down and install a wet bolt kit at the same time. Another option for a mild lift (2-3", max) is simply to have longer, heavy-duty, spring hangars made. The couple I've seen on here have also had cross-bracing for extra strength. Short of that, a sub-frame welded between the frame and springs is the only truly safe way to raise it. Steps aren't that expensive, so that really shouldn't be much of a factor.
Lyle