I think the best reason for doing it is just to be different. On my frames I've mounted brakes (in addition to the traditional location) under the seat stays and on top and under the chainstays. I do it mainly because I like the clean look of a "bare" seatstay... makes people wonder and scratch their heads.
On "handmade" frames you only have so many opportunities to be different. That's what you see at NAHBS.
Others do it for different reasons. I think Rob English (English Cycles) does it for aero. Look at some of his examples. Brilliant! Neat cable routing too. These are mainly race bikes where "dirtiness" is not an issue, though I'm not certain a rear brake mounted anywhere is any cleaner than anywhere else. If you didn't see his stuff while in SAC you missed something special.