Power-Taps are most valuable in training. Put it on the machine you do the bulk of your training on. It sounds like for you that would be a tough call. I would lean towards the road bike which is the best machine for specific intervals. It is on the specific power interval sessions and the field testing sessions a power-tap is most useful.
If you race a 29er mtb you might be able to get a single 29er power-tap to fit on a cyclo-cross bike and a 29er mtb. Then use the cx bike for the road riding.
Lynda