I expect my car to start and drive when the fuel indicator indicates 50% fuel (or 50% charge in the case of an electric car). The indicator doesnt have to be perfect, if I keep driving with a warning light, I'll take the blame, the estimated range may be off, but If it stalls on the highway with an indicated 50% capacity, I blame the manufacturer, not the driver for not fueling or charging his car. OP never even got a low battery warning.
You are confused or confusing. No battery will deliver nominal voltage when its depleted, even with no load. Take any empty lipo battery, and you will get something like 3.2v per cell, no where near 4.2. The opposite is just as true, if your lipo battery delivers 4.2V with no load, its fully charged, always. It may be faulty, but its as full as it gets.
Now voltage will sag when under load, that is true. Voltage under load therefore doesnt correlate directly with capacity. But especially on a quadcopter, that load is fairly constant and predictable. Not only that, the load is actually measured and the voltage sag is known and taken in to account. A simple voltage reading needs context; 3.8v at rest is only half full, 3.8 under high load might be a full battery. But that is why we typically dont get to see voltage, instead a calculated value. Its like that with just about everything, including your phone. Which I bet, doesnt suddenly turn off even though it says 50% battery left. In this case, it was WAY off.
What are you talking about, "100% E" ? His cell voltage on take off was ~3.6v. Thats no where near fully charged, even under maximum load. If it was, then the battery has an inadequate C rating. A fully charged battery is 4.2v per cell. That may sag to 3.9 or so under peak load. Not 3.6. He took off with a nearly depleted battery, and for some reason, the software didnt read it as such, even though anyone could tell just by looking at the same voltage values that the software saw.
Thats in no way weirder than indicating 56% for a battery that couldnt possibly have that much capacity left.