Will the roof of the alcove be the same height as the roof of the camper's main body, or will they be at different heights? (See @IdaSHO 's camper photo in the quote below.) If the alcove and main body will have the same roof height, that may result in an camper's main body interior height greater than you are currently thinking. Keep in mind that having enough height in the sleeping alcove can be quite useful.
Being able to wear boots and a hat inside without scraping the ceiling might be useful to you.
You don't have to match the camper's main body to the flatbed, but I suggest you have good reasons for exceeding the flatbed dimensions, and keep in mind that you might want a good bumper protecting the rear of your camper.
The roofline is flat. We aren't cowpolks so I don't think we'll need boots or hat clearance, lol. We want to match the dimensions of the flatbed to minimize overhangs, etc. I intend to use the stake pockets on the side as rub rails.
Anyhow, since this is the final dimension check off, I was looking at everything more closely and realized that the vertical height in the cabover is only 29". I guess I'm going to need to have the headache rack trimmed to either be flush with the roofline or just remove the upper portion altogether. Our Airtop has around 37" of clearance and we could probably tolerate a little closer since we could stand up elsewhere.
Below are some of the dimensions from the builder (in mm, of course):
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