i run it up with the headache, just hangs off a wire for like 8-9 years now... but if you run it low or flat on the deck for some reason cover it up with a hd steel cover for sure. keep water out. what ever you do make sure its protected from constant water spray or water exposure in case the cap gets left off or whatever...
i can run it under rail as i have a higher then wanted deck height, but i raised my gas tank as well and installed a 34 gallon unit.
take a long hard look at the situation and make the truck better for you if you are taking the time to make a flat bed. slide out under bed stowage....crane mount and maximal surface area and bedside options for carrying various materials will dictate design of floor toolbox and bedside mounts.
flatbeds can work really well or be all but useless if you build them without adequate tie points and bedside options. i can fit 4 motorcycles in mine and all the gear depending on what panels i am using.
the flat bed was one of the best mods i ever done. wish i would have built it the first day i had the truck. i have two metal drops and wood on the deck, a metal deck with a rubber mat is where i will likely end up as a permanent floor at least that is what i was thinking back in 08 or so
.......my sheet wood deck buckles when not laden after a week or so of sitting.
i went to the raised deck mainly to allow for my monster fuel tank, tire size variables....and under bed stowage.
made from free scrap metal to boot save for the headache.
i beat it to death. but i really encourage you to take your time designing it and look around at all the creations off road and on if you have not already...overlander guys, construction guys..ect. if you have or are considering a slide in camper, that will have bearing on actual bed height to cab ht ect....
i really wish i would have built one right off the bat. put a little thought into it and i am positive you will be wishing you had done it sooner.