I knew there’s some across the bay, but they sure hide the other two stores in SF. Never seen them even show up on their genius bar search.
Are they official Apple stores or are they apple-branded franchise stores? Reason I ask is because that’s the model I’ve seen a lot in Europe. A store that has a license to be an apple store but isn’t actually owned and run by Apple.
They are real Apple stores. Short of dedicating a downtown city block to an Apple store, there probably isn't any way to fix the capacity problems at the OG SF store so, as you've found out, it's best avoided.
There are three Apple stores in SF proper and a couple just across the bay.