I also hate the way Durock crumbles, but I equally hate having to cut any cementitious board when drywall will do just fine. (And by the way, green board or other such things are a waste of time and money IMO.) Even in showers I rarely use CBs - I put Kerdi over drywall, or I use Kerdi Board.
As for building up a mud floor, "passe" is one word used above. A massive pain in the neck and outdated and unnecessary are others. If you need to raise the level of the floor to match old transition heights, just use plywood. If you need more structural support, again just use plywood. In theory it's probably best if the dyywall is slightly raised off the plywood about a quarter inch. For the floor I would use Ditra, or Ditra XL if you need more height. There are other uncoupling membranes out there made by Laticrete, Mapei, and Custom as well which should perform the same (unless you want waterproofing). Any of them are better choices than CBs, which I basically avoid when I can. If you do use cement boards, I would use the 1/4" Hardi instead of 1/2" Durock.