If Mike Van Pelt asked for this thread, them I'm going to narrow my focus and assume that we're talking about a GXV truck.
I like that it's a hard-side. If you're going to build a lifting roof from scratch, might as well go with a hard-side. Also GXV has already got the engineering done, for their Pangea model, and the overall construction is also right up GXV's alley.
With the top down, it's still usable. Inside height with the top down is 5', which is roughly the same as a full-size conventional van with a 6" or so raised roof. Ala Roadtrek:
So, even with the top down, it's still a very usable space. Even the head can be used as long as you don't mind sitting down to use it. The shower...probably not with the top down, unless it's a full wet bath and again, you don't mind sitting to use it.
For stealth and security, I like that with the top down, the windows disappear. For security, what I don't like, is that with the top down, the windows disappear. If I were sleeping in a place where I'd want the top down for security, then that's probably exactly where I'd want the ability to see what's going on outside. Shouldn't be a big deal though to rig blind spot cameras. The truck almost certainly needs a backup cam anyway. Might as well just go whole hog and add a 4th cam to see what's going on in front (put it up high with a fisheye lens, and you might also be able to use it to see if you are going to make it under that low-hanging obstacle).
With the top down, it doesn't really look like a camper, except for the hatches and that big entry door. I think those could be camouflaged to make the truck resemble a work truck. For weekending, probably not needed, but for long term, long distance use it might be a good idea.
Crawl through...probably not. Looking at the first pic in this post, it appears that there *might* be enough space under the roof to make a crawl though without the boot interfering with the roof...but it would certainly be tight. One way around that would be a gangway/mudroom between the cab and cabin, with a drop-side stairway.
That would also allow the door to be moved to the front, which has two main drawbacks: First, the door has to be a two-piece ala Alaskan. But that's not a big deal - in fact, it's good for ventilation by leaving the top part open, and besides Stephen Stewart recommends a dutch door anyway for security reasons. The other (possibly big deal) drawback is you lose 3' or so of "living space". You do regain part of the living space though by not having a side door, and the port side of the mudroom could be a 3' wide x 2' deep x 5' high storage/utility box, possibly with the generator and/or batteries in the bottom, though I'd rather have the batteries down between the frame rails.
The truck *might* fit in a container. If not, then the use of container wheels would probably be enough to get the job done. If not, then the camper box in the first pic is removable. It sits on a flatbed. I like the idea of a removable camper box. It doesn't have to sit on a flatbed, but I think taking remove-ability into the initial engineering is a good idea. I particularly like the way Darrin Fink does it, which I believe he does by incorporating 2" receivers into the frame of the camper box and using standard camper jacks:
Add some receivers in the frame pointing down, then lift the box, drive the truck out, stick wheels in the bottom receivers, drop it down on its wheels and pull the jacks out of the sides. Then use the truck to shove it into the container. Lash it down, then drive the truck in right after it, ala that 6x6 Unicat Mog.
I think the lifting mechanism is important as well. There are a lot of different ways to do it, from Alaskan's hydraulics to the 4 electric screws jacks used in the camper in the first pic (which, using a 4 switch controller, allows the owner to tilt the roof a bit this way and that to direct rain runoff where he wants it), to a recent post by whalecharterboat (All Terrain Warriors) describing a setup with 4 pneumatic power up/down rams and equalizing valves. The (gorgeous) Bullet XV uses hydraulics, with a system of cables and pulleys (maylines) to keep everything synced:
Personally, if I was building my own from scratch, I'd go with a screw jack system similar to this:
Though, of course, it would be much less heavy duty and I'd use "traveling nut" jacks rather than "traveling screw" jacks, but you see what I mean. The driveshafts and 90 degree transmissions could be incorporated into the camper frame, the roof attached to the traveling nuts, and, it could even have a hand crank for use in a pinch. (And of course the motor doesn't have to be in the center...I'd likely stick it on the end of one leg of the "U" and delete the center transmission.)
There are several advantages, such as the roof goes up square regardless of uneven loading, even thin light duty screw jacks can lift a lot (roof + stuff), it stays where it's put (you could even drive with the roof up if you had to), it isn't going to leak and need new seals, it doesn't require locking pins to prevent creeping and when the roof is down, it's down "and locked". [EDIT: And...it's quiet.]
Also, it's mechanically pretty simple and bulletproof (yea, that was a pun about the maylines ).
[EDIT AGAIN: Also, forgot to mention: Since it's a mechanically synced system, and the roof is always perfectly square to the bottom box - two-piece overlapping interior partition walls are not a problem. I.e., you can have a head with walls and a door instead of just a curtain.]
A box like that could be mounted on a brand new Fuso FG, or on a refurbed surplus Mog (smaller Mogs, like maybe the commonly available 1300) or several other platforms.
I think GXV could probably sell a few...especially if they could do it at 1/4 - 1/2 the price of a bigger rig.