^, ^^ For #1 and #2, I think the issues can be addressed with design. For eg our camper was made with the LPG and water storage located above the height of the pick up box rail. Our camper deck allowed them to be relocated lower. Some pop ups have storage space in overhead cabinets or under the over cab bed. A flatbed camper design can make possible locating that storage lower. And the flat deck itself could possibly be built with things like batteries, water and extra fuel to be carried under the deck surface, same for under deck storage boxes. 'Course all this FB storage means a heavier, bigger rig so I don't think the extra height has as much of an affect, unless you're doing it all with a small truck.
That said, truth, if you just put a deck on, yeah, it's gonna be higher - ours is.
Thinking about this ... if we're talking 65K for a camper and 5 or 10K for a deck (my expectation) I think I'd be looking to address these issues with a frame mounted camper design. Kinda like what Provan did. Doubt there is a business case for it but IMO it could look and work better than a deck + FB setup and the side door (much preferred) could be put lower than with the flat deck version, which usually look way high to me and fido.
I'm also not sure how much value a stand alone flat deck gives to a pleasure use owner. At these dollars I wonder if the purchaser would likely be buying a dedicated RV anyway ??
Three disadvantages of a flatbed camper I observed from borrowing one is that:
1. It messes up the fuel (and DEF for diesel) filler tubes which makes refueling a pain because the filler is lower and more horizontal.
2. Of less importance but still with noting is that the flatbed is a couple inches higher than the floor of the original box. This raises the COG, raises overall vehicle height, and makes getting into the camper more work.
3. Adds $2k to $6k+ to the cost.
There are significant advantages to a flatbed of course, and I was convinced I wanted one until I used it.