The Legacy commands are repeated, and it would be way more complex to find a null point in the TMCC/Legacy signal stream, so I think that's a needless complication. I suspect the TMCC/Legacy commands will get through just fine.
Since the TMCC/Legacy carrier is constant and uses frequency shift encoding, it would be fairly complicated to find a hole. Also, if you were trying to synchronize the two, it's likely you'd be missing DCS commands. If there is a conflict, who gets priority? Since the DCS commands only use a very small amount of the bandwidth, it's far more logical to interrupt the continuous carrier of the Legacy signal as opposed to the DCS packets.