I just remembered something else...
I took one of my chickens to my vet a few years back as she had a sniffle. The vet bought all the nurses in so they could experience handling a chicken as he had never treated one before.
'Pet' hens are a fairly new thing and a few, kept well and very clean, in a garden are going to have far fewer diseases and germs than hens raised in vast commercial units. Comparing pets with commercial conditions might explain why your vet raised concerns.