A fold down gate at the back mounted to the bumper might be a way to go for the bike, how heavy is it? Lots of campers have a sliding window and a boot from the cab to camper, maybe that would work for the pass though. Otherwise, the front of the camper would require considerable remodling for a walk through......Have you thought of an "interim" camper to try out some concepts, and solidify your design for a custom built unit?
The bike weighs in at about 250lbs.
If I went through with the pass-through idea someday, I would like to remove the center seat/console, remove the middle portion of the rear sliding window, Cut and re-enforce the sheetmetal of the backside of the cab, from the bottom of the window to the floor, and make appropriate modifications to camper.
If the camper was off I could seal it up with some plexiglass and door seals. But I'm getting ahead of myself here, this is why this projects gotta be down the road

Yeah lately I've been warming up to the idea of buying a cheaper camper to get some experience, see what I need, and what I don't. I'll probably go that route, cause at this rate my designs of a custom rig will take forever to turn into reality, lol.
Visual learner here. You mean a short pop-up which leaves you with 24" of bed space at the rear, correct? That's not a bad idea but I agree with docdave....go for a camper that fits the length of your bed (provided your truck can haul the weight) so you're as comfortable as possible in the camper after a tough day of riding. Use a hitch-mounted moto-hauler to carry the bike. The XR200R can't be all that heavy. What's the tongue weight rating on your hitch?
Also, if you're dead set on the short camper in a longer bed, you'll still be able to run the toolboxes along the side if you install a flatbed.
Hopefully we're making sense to you. I think you're onto something slick which will open up a whole new chapter of riding. Have fun!
Musta been tire when I wrote that last reply, I was thinking of my 10' flatbed, vs. 8' bed, but I forgot lots of the campers hang out a couple feet anyway, so it'll probably just be flush with the rear bumper. Which leaves me with the motorcycle mount using the receiver hitch idea. Tongue weight rating of about 500lbs.