That may well be true, but whether they charge a diver a flat rate per fill, or by the cubic foot, the odds are they are ripping that diver off by stopping at 3000 psi and then leaving the diver with only 2800 psi when it cools to room temp. Assuming you started with 500 psi and left with 2,800 psi (after it cooled) that's only 71.8 cu ft not 77 for a final volume, and it's only 59 cu ft actually pumped, not 64 cu ft. So the diver got shorted 5 cu ft, no matter how he was charged for the fill.I get the impression that shops consider that higher pressure air needed to overshoot as compensation for cooling to be more expensive and don't want to deplete their banks.
As much as possible I leave them so I can get a final top-off before I take them.
It's true that the last 200-300 psi to get an honest fill comes off the top and will lower the bank pressure, but if you think about it, taking another 5 cu ft off the bottom of the bank would reduce the bank pressure by the same amount and require exactly the same amount of compressor time to refill the bank to the original pressure, so it's not about saving PSI, it's about releasing less gas from the bank in total - i.e. screwing the customer who has a 3000 psi tank and should get a full 3000 psi fill.
Kudos to you for expecting the shop to do that. The shop may have come to expect it, but if they understood the bigger picture, they'd just hot fill your tank to 3300 psi to start with and save the staff time and gas lost in connecting, disconnecting, reconnecting and disconnecting your tank for a fill and a top off.