As many of us have said, vets and those who work there, (exceptions to those on here) know very little about dog behaviour.
Some people are very strict with their animals, I commend you for speaking out to her face to face with what happend.

Shouting in a practise is likely to upset other animals there, the poor dog being examined whilst hearing the nurse shout at the dog must have been feeling extremely nervous aswell, and it was extremely unproffessional to examine a dog in the reception area, short staffed or not. The dog concerned would be better off in the kennels for the day rather than being asked to be a carpet rug under the reception desk, obviously not wanted there, when it purely was not the sort to just lounge around with no interest in what is going on.
If a dog were every misunderstood it is that one.
I would never return to that vet, but agree you should report this incident, if not for the sake of the dog not being brought to a place where it is treated as a hinderance.