Apple does, and their employees do as well. I was directed to the Scottsdale Flagship store by a store manager.
But I agree that it is odd how they're stocking.
Yeah, I’m sure you’re right, maybe it varies on the store, who you’re talking to, etc. and we are using the term ‘flagship’, then I would say I have two of them in my geographic area, but I just never heard it referred to as by Apple employees, ect.