There have been some frames designed to work with both wheels, I forget exactly who or why. Presumably something like a touring bike that could bale out onto locally available parts, or be configured for mud and road. Nashbar used to sell a touring frame (new model this year). That had a BB height of 13" in 700C. If it were set up for disc brakes, it would seem possible to switch wheels without much adverse effect, which sorta makes LW's point since a 13" BB height is very high.
Another option is 650B, In that case one can use adjustable V brakes as well as discs with the two sets of wheels.