I think you've got all you questions answered, and if I'm understanding correctly, you want the flat bed and understand it well.
So, I'll say go to All Terrain Campers, work with Marty and Jeff, they will do the things you want/need that FWC won't do and usually at a better price. They did a nice job for me with my custom requests for my Bobcat shell in my regular truck bed. I didn't need the newest advances that FWC offers, and FWC didn't want to make any changes to meet my needs.
When you fabricate the flat bed, try to make it a "standard" flat bed size, if that exists, it will be easier to sell the camper, if ever, later. I don't think you'll have any issue with selling it. Granted there are possibly fewer people that may want one, or could use one, however, there are also not that many out there, so, I think it will be a wash. Advertise it in the right geographic place, where there are plenty of outdoors-men with flat beds, and they will be knocking down your door.
After you've made the flat bed, Marty and Jeff can make the required foot print measurements (if you're close enough to take it by their shop), or talk to them before you start to build the flat bed (they may have some "input" for you), and you'll be "on the way". You may even want to touch base with Marty and Jeff to see what they recommend for the camper mounting technique, before you build the flat bed. I'm sure they have some good ideas, and if your' ideas are better (in your mind) they will work with you to figure it all out.
In any case, start building a relationship and partnership with Marty and Jeff on your project.