Understand that I'm not saying you are doing anything wrong, but if he's doing it exactly as you describe...he's doing it wrong
I get that 100%.
Here is how it goes in the small local shop I frequent. They are usually sitting (or standing) right next to me as I fill out the 4473 and they are going over it and inputting the needed information into the online NICS at the same time. And They have does this right in front of ATF agents too. I'm not saying it is right or wrong either, but that is how that shop does things at least with me. I have known them a long time and I always have my UPIN and valid CCW with me. No Missouri CCW permits are not exempt from the NICS check.
Now I don't expect this to happen in a big box store like Bass Pro, Academy, etc.