Ed, I'm just a newbie builder myself. Prone to offering advice above my experience level. That's a nice profile you have in mind. I'd vote to keep the flip.
Agree that it'll be more comfortable to have the door start just a couple inches above the floor.
Not so sure I agree the rear flip below the floor will be hard to do. It's a nice design detail and would be nice to keep, if it's not too much trouble. It looks like its all below the floor so in my estimation it shouldn't be all that hard to build. You could insulate the floor under the sleeping area and skip insulating under the flip. If you do an insulated sandwich floor - do the back part with just a plywood floor without the thicker floor "sandwich" in the flip area.
If your side wall is built with a Dado Joint you could cut out the flip from the rear part of the cleat and sidewall plywood below the floor. Have the steel trailer frame end about where the flip begins. Actually you could probably do it just as well with the Lap, Rabbet, or the Dado.