If you are nordo, how would you know WHEN to wag any control surfaces???
That's why the first word of the instruction is "If."
For tower OPS, there is a light gun process in acknowledging ATC and they can use the light gun for ground OPS, but that comes from tower, not ground.
Ummm...just where do you think the ground controller is? That's why towers are tall, and located where (hopefully) all the movement areas can be seen from.
You use your lights or control surfaces or even your transponder IDENT in the case where you may be able to hear but not transmit.
And if you are facing away from the tower, or if the airport doesn't have ground movement radar, how would you acknowledge the instruction?
Like others have stated, it's an option that can be used when trying to communicate with a NORDO aircraft. Would it have been clearer if the controller had said "...move your control surfaces/flaps?" "Rock your wings" is pretty standard in a VFR tower environment, so most pilots understand it.
FWIW, there is actually a prescribed phraseology in FAA Order 7110.65, that says "If you hear (facility name), ident." Over 19 yeasr in the business, and I can't figure out why we just can't say "Ident." If the pilot hears it, he will. If he doesn't, he won't. Pretty simple.