Putting a TVS internally across the motor will have no effect on any command signals, DCS or TMCC/Legacy. Obviously, if you don't now, and never intend to run DCS, then you can sprinkle those TVS diodes anywhere you like.
To paraphrase: "What happens inside the electronic package stays inside the electronic package". 
One issue with a truly huge ton of TVS diodes all over the layout. Although they don't fail often, they do fail. If you have twenty TVS diodes distributed around your track, eventually you will have a failure of at least one. Tracking it down might be a bit time consuming.
