Just to add to the conversation, I routinely haul a lifted 4 seater Club Car Onward golf cart in the bed of my truck while its being towed behind my motorhome. I have the 6'4" bed, and the rear wheels of the golf cart straddle the gap between the bed of the truck and the tailgate, so you are 100% correct that with your shorter bed, the tailgate will need to be down. I purposely bought the lifted cart so that I can drive it up into the bed of the truck without having to back up to a berm or back down into a ditch when loading/unloading. With that being said, I didn't want to rely strictly on the tailgate cables to carry the weight of the cart, I purchased a set of
DG Manufacturing Support Bars for overall support. And with the lifted cart, I can load/unload from flat ground and worry about the rear of the cart bottoming out on the ground as it climbs into the truck bed.
Be careful with the ramps you choose... I looked at all kinds of solutions prior to buying anything. If you purchase the hinged ramps, that will cut down on your weight capacity. I went with the one piece Reese Explore Ramps with the 3000lb capacity. They are made out of aluminum and are only 39lbs overall. I just slide them underneath the cart while traveling.
Not sure what pop up you have, and how long the tongue is and how tall the front of the "box" is. But depending on how long the overall cart is (if you have a rear seat and floorboard on your cart) once its in the truck, you may not have enough room to make turns without the corners of the tailgate hitting the camper. Also, if you have a tongue jack, how tall is it, and will it hit the underside of the tailgate when you go up into driveways.
I know you mentioned using a hitch extension, but I'm thinking the length you would need is going to be too long to safely do what you are trying to do.
