Does brake modulation matter, for efficiency, beyond having enough to avoid locking the wheels?
You say "Surely the brakes should always be used to near maximum stopping power". This is where the first need for modulation comes from. Stopping power has at least as much to do with grip between the wheel and the road than the torque your brakes can except on the wheel. Maximum stopping power comes from the front wheel (plenty of discussion about that here) and you really want that to not skid. Thus you need to modulate the front brake if you're riding on varying surfaces. Similarly if for some reason you need to brake on a bend, you'd better make it gentle. In both these cases pulsing the brakes at a humanly-feasible frequency won't help - the initial loss of traction when you jam them on its what will start the skid. I don't think you can assume perfect or even constant grip anywhere let alone on a trail. Think of leaves on a packed surface - the grip can deteriorate with little to no visible change.  A bike set up for one set of conditions will be used in a variety. By using your brakes only at max strength (which would have to be quite high) you're removing a useful degree of freedom. 

Riding in traffic - as you may do on any bike, even if just to get to a trail. you may want to go slowly to catch a gap or just because you're stuck in a queue. Your pulsing technique would work better here, however it makes for a very jerky ride - not what you want if one hand is off the bars to signal, especially if it's the hand that works your front brake. It wouldn't really be a good idea to set up a MTB that couldn't brake gently. In design you also have to assume a rider who is inexperienced of unfamiliar with the conditions; the latter especially may want to brake progressively which requires modulation.