I'd just wire the TT to a switch that switches between the conventional and command power sources. The actual tracks inside the roundhouse would be dedicated to a particular type, or they could be individually switched between the two if you wanted flexibility in using each bay for command or conventional.
I don't see any particular issue with running both using one TT.
Obviously, the track(s) coming up to the TT will have to reflect your operating mode, are you having a single track coming in, or two?