I had pretty much the same experience. When I went to the PP boutique, I had an old patek on and asked them to open it/get the ref. number. Although the gentleman helped me, the store was empty and it didnt seem like anyone was very happy I was there. I felt uncomfortable based on my age, which was BS given that a non-trivial chunk of their business (at that location) was russian kids around my age. I didnt feel comfortable asking to see some of the very rare watches they had there (which I now regret). AP was great- as you described. It didnt have any sort of museum feel to it, but I didnt expect it to.
VC was very laid back- the guy was very helpful, nice, and unpretentious- he was very excited to show me the redesigned overseas (this was a couple years ago). Roger Dubuis was a very nice looking store- when the lady saw I wasnt going to buy ten watches for cash, she lost interest in speaking to me- she also wasnt particularly knowledgable. I have to say, my BEST experience with a brand store was the GP boutique in gstaad- the couple that ran the store were absolutely terrific- knowledgable, nice, passionate. They later set up a factory tour for me and some friends which was one of my greatest memories from switzerland- it definitely gave me a lot of respect for GP and it will be a on my mind whenever i consider buying a watch as a result.
As was discussed in the Rolf Schnyder interview, a brand store is advertising. My experiences at these stores has contributed to my views of the brands. And if I have a particularly bad/good experience, I will no doubt hold on to it and have it affect my purchases.