There is certainly some tech analysis that Tesla has in its battery energy measuring that goes deeper than my understanding. There is some aspect of it that is based on the cell voltage, but there is also some part that is trying to keep track of energy in and out, so some very smart combination of all of that. That seems to be part of the reason why the energy estimator gets confused over time and loses visibility if you continually stay in a middle state of charge. The voltage just doesn't change much over a large section in the middle, so it doesn't get to see that voltage shift to really tell when it is getting actually high or low, so it's lacking one of its measurement methods.
So anyway, that is how it tries to figure the current amount of energy. And it does keep an internal number that is stored in a variable called something like "nominal full pack energy", where it stores what it thinks the current maximum kilowatt hours value is. And that's how it tells the %, by comparing current energy versus that apparent maximum capacity.
