These units are typically built with the floor covering laid throughout as part of the floor manufacturing, and then the interior walls and furniture are installed over. So your floor should be continuous, but now with a few screw holes which can easily be filled with vinyl floor putty to match. I did a major renovation of a bunk room in my in-laws fiver. The floor extended all the way into the floor of the outdoor kitchen (most of which I reclaimed for the rear room) so it was continuous.
Go for it. Good luck.
But I might recommend a shallow false wall around the lower area where the exterior pas me through doors are. This way you can still store small stuff from outside and keep the hot/cold air out better.
2016 Voltage 3305
2002 F350 SRW 7.3L Turbo Diesel