I highly doub your going to find a cap the atv will fit under, as you have to think about the handle bars, as both you drive up the ramp and into the truck, and most atv,'s the rear rack when in bed of short bed truck will be hitting the rear window on the cap
I have a leer cap on my 2016 ram 2500 a MID rise cap and its not even in the ball park of clearing an atv, a HIGH rise , won't make that much of a difference IMO
NOW if you run taller tires, that will add even more fitment issues into it fitting into bed and allowing tailgate to even close with it in there!, plus WATCH the front of atv so as NOT to poop your window out the back on bumps and such!
if you have a HD truck they DO sell ATV hitch haulers, I never used one, but have seen some that do, some trucks will support up to 1,000 lbs on the hitch like set up
a LOT of tongue weight for sure, but can maybe save you from hauling a trailer, if you do this, watch your approach and departure angles when driving!
a trailer just makes hings simpler here , to be honest!
as even if you get atv in bed with a cap on, there isn;t much room for anything in bed after that any how, will become a nite mare getting things out that slide under it or between sides of bed and tires
and a trailer will see a lot more use, call it an investment?