Trained staff, health inspectors and dishwashers solved all of this.
Some friendliness on the part of the establishment as well as good judgement on the part of the employees are enough to gloss over size differences in cups. Most travel mugs you see are going to largely conform to your typical to go cups, and nobody really bats an eye at filling a 14 oz cup and charging it as a 12 oz instead of a 16 oz, but if you fork over a 48 oz monster sized mug, you’re probably going to be charged for more than the large cup size and should expect it. How much more depends on the establishment, but at my old job I probably would have charged you for two 20 oz cups and not given a crap about the spare 8 oz, and if I had to answer to my boss, then most likely he would say he would have done the same.
It’s more important to cultivate good customer relations than to nitpick about exact cup sizes. You want repeat, regular customers giving you a constant revenue stream and you’re not going to get that by interrogating them on precisely how much coffee fits in their damn travel mug.