Will the DCS Commander Control (50-1028) Operate ANY P-3 Features?

As long as it's been previously reset to factory defaults, my information says yes.

The 2012 RTR sets have PS-3 engines and the Remote Commander.

I'm sure there would have been an uproar here if they didn't work together.

I believe that should put the question to rest.

The REMOTE commander does not give you access to all DCS featires.  i.e. You cant control smoke volume with the remote. There are many more you cant get on the remote commander

Larry is right.

The Remote commander will do:

Bell On/Off

Sound trigger (activates a (random?) sound from the list in the engine (Idle sounds anyway)

Power Up/Down

PSA start (use Dir button to cycle thru the sequence)

Speed up/Down in 1 SMPH increments or faster if held down

Whistle

Coupler (then hit + for front or - for back)

Volume (+ or - to step up or down)

Direction (cycles Fwd, Neu, Rev, Neu as normal)

My question was specifically for the DCS Commander Control BOX, and NOT the remote.

Will the 50-1028 (the BOX) operate many of the P 3.0 features?

The DCS Commander should operate them fine, subject to the limitations it has.  I don't think it does MU consists, for instance.