Twice now I've had the clerk do this to me.
In my cases, though, they weren't so attentive from the beginning, like the OP. I got my ReadyPost package just fine, and had my item all sealed and addressed and all that, without drawing any attention. It's just that at the counter, the clerk said, "Hey, I think I can save you a few bucks!" and stuffed the whole shebang into a flat-rate Priority envelope, and had me do a new label. They just *insisted* on saving me money, darn them!
Anyway, yes, I did get paid. I explained the whole thing in the report, and also used the 'contact' link from the shop log to send an extra note to the scheduler. He said it would be just fine.
It's not like *I* did anything wrong. Scheduler confirmed that if I'd put up a fuss or rejected what the clerk was doing, I'd just look like a weirdo ~ or a mystery shopper.
Practitioner of the Nerdly Arts.