I can safely say- from building an actual stick-and-brick how, you will never know entirely what you want. Light switches will be in the wrong place, or another window here, or not one here, etc.
That said, I can only imagine that ordering a 100% custom unit is spendy as heck. Could be worthwhile to have something built that is almost exactly what you want. I've had a design in my mind for a while, but couldn't justify a custom build unless I tried to build it myself (w/ help, of course).