"they should apply to everything."
Well that seems based purely on consistency, and I just disagree with that. I'm all for outlawing (or heavily taxing) newly produced, loud motorcycles, but it's not a hill I want to die on. Internal combustion is a fading technology anyway.
Remember that internal combustion replaced horses, which at one time covered city streets in massive amounts of manure. As new transportation technology arrived, should we have just said "anything that is equal or better than tons of horse crap is A-ok"? Or should we hold new technology to higher standards, while letting the annoying old stuff fade away on its own?
"Drones aren't going to come any more often than delivery trucks do today"
I find that an odd assumption. If the cost gets low enough, as it will, you'll have people ordering drone-delivered trivially small purchases that they want delivered immediately, such as cups of coffee. Meanwhile, the frequency of loud motorcycles will get less and less, as electric vehicles become more common over the next few decades.
If it were up to me, drone deliveries would just have to pay an annoyance tax, to compensate. This would create an economic incentive to develop other alternatives, such as robotic deliveries that roll on the ground.... which to me makes far more sense anyway, since they aren't spending most of their energy simply keeping themselves airborne as drones do.