The big custom coach manufacturers, like Foretravel, Newell, and the various Prevost conversion companies, will do a totally custom floorplan for you. Figure $1.5M and up for that, from scratch.
Newmar will do a fair amount of customization, but probably won't change the basic layout (kitchen and bath locations, slide size). I think they'll do more than the other manufacturers in their class (Tiffin, Monaco, Entegra, etc).
2008 King Aire 4562, Spartan K3(GT) w/ Cummins ISX, Motosat HD-SL5 w/ SWM-8, Multiswitch, HR34 Genie
2014 Jeep Grand Cherokee Overland 5.7L V8 Hemi w/ Blue Ox Aventa LX Tow Bar and baseplate, SMI Air Force One brake