(I think you are overthinking this. I have the B&W RVK3600 set to lowest setting and use Alt ride mode ALL the time with ZERO issues. Just use the Transport mode when unhitching that should resolve all your issues.)
Don't mean to hijack the thread but 12V98, how do you use the alt ride height ALL the time? Mine will go back to normal ride height after removing load when you start to drive it.
As to the OP'S question, If your hitch was that low in the bed I can't see how you would have any rail clearance unless your pin is really low on the trailer, at 17 inches on the hitch I have about 6in of rail clearance.