Yes, I stay with one boutique. Your purchase history is tracked at each store. While the SA can be nice and super helpful, he is not the decision maker when it comes to one off needs. It helps to know the store manager.
One time, I purchased a ring at the boutique after trying on two sizes. I have to fly to visit the boutique. After I got home, I was second guessing myself thinking I should have chosen the smaller size ring. VCA boutiques technically only give store credit for returns. The manager authorized my SA to allow me to get the second ring, try both on at home, and mail back the one that did not fit with a full refund on the one I sent back. Little things like this, and of course when they think of you for some perks.
In the end, this is just sales. From a business perspective, the boutique is all about performance... which SA sells the most and which client buys the most. From a client perspective, the SA has his list of top spending/favorite clients, and the boutique/boutique manager has their ranking of clients. VCA at the top tracks how each store is performing, the top VCA spenders. Everything is measured and rolls up. It's just the nature of sales and business. A key rule in business is to "protect your base" (e.g. focus on your repeat clients as they are your base for revenue). My SA told me he has a spreadsheet of each of his clients, from their spend, to their likes/dislikes. I love that, as now, I don't need to keep training him on my preferences. The boutique knowing me and helping me is what I value, which in return, I give them my repeat business.
That said, sales is a two-way street, and we are the client. If you cannot get what you want from your SA/boutique, I would definitely find another. If you are happy with the two boutiques you use and they get you everything, I would keep it that way. It's what works the best for each person. There are ladies in this forum that shop with different SAs in different boutiques, and it works for them.
It's all preference. It sounds like you are local to the new SF store. You are so lucky to have a local store!