Actually, the amount of drag might be less. You're actually moving your TX stick to get the result you wish. If you wish to roll the airplane slowly, for example, you're only going to move the TX's aileron stick whatever amount that makes the airplane roll as slowly as you wish. If only the ailerons moved to get that slow roll, they'd move a certain amount to do it. If both they and the flaps moved, then they'd move less, right.

There are a number of different aerodynamic "things" involved, but having the "longer" and larger surface move less to get the desired result would probably get the result a bit more efficiently. So there might actually be less drag.