No problems (except slower wheel change).

why slower wheel change?

The MTB frame is 135mm wide and the road hub is 130mm.
You'll probably have to "compress" the frame slightly while you put the dropouts onto the axle ends, or it will drop down onto the 5mm quick release rod.

So not ideal when fixing a flat in a race, but doable.

Another thing, you don't need a "29er" rim. A road rim works fine for your MTB (or CX for that matter).
I've been preaching this solution for a long time. One powermeter that does training&racing road, TT (with cover), CX and non discbrake 29er MTB. No other PM can do that.

sounds pretty sweet. now the trick is finding a lightweight Alu 29er frame that still has V-brake mounts!?

Another option is to find a nice CX frame with enough "mud clearance" to fit a 2.1" 29er MTB tire...
Up front you can swap between a carbon CX fork and a "short stroke" MTB suspension fork. Maybe..