good news is, you are suppose to use the throttle on demand, as you are, that's the whole purpose of it.
personally from your choices i'm using option c) set Assist level 1, as Assist level ZERO is pretty much off, and you are carrying nearly 11 lbs of dead weight (battery + motor hub)
is not really bad, if you only plan to use the throttle whenever you feel like it, and do everything else on your own.
I'm rather a speed maniac, so the minimum level of assist helps me get through the wind, and hills without losing momentum.
for the very same reason why i ditched my car for the bike, as in rush hour a car is pretty much useless, and i hate bumper to bumper rides.
so a bike is the best, as it can zip through places even a Gas Motorcycle is not allowed to go through
and yes my 1 way trip is also 25mile each way, so a round trip is 50mi a day.
before that, i was doing my commute without BionX, but since i moved... it turn into a rather agonizing ride doing 50mi every day.
now with BionX is like back to normal, you still pedal, you still sweat, just not extremely exhausted when you get home.
Dahon Matrix + Jammer GT aero bar + BionX PL350 (17 lb) + Topeak A rack & DXP bag (2.66lb) + fenders + 165lb of BioMass.
cargo contents vary day by day (clothing / food / supplies / drinks)
Bike total mass weight is approx 55 lb + me + cargo (average 5 lb), so grand total hauling of approx 225 lb