The factory tour and the Friends & Family sale are completely different. If they do have a sale in 2012 (they did not in 2010), then it will probably be on a Saturday morning, as the last two have been. For the sale, they have demonstrator, prototype and overstock guitars. You never know exactly what will be there, and they don't post a list of the guitars available. But in my experience there's a fair selection from across the spectrum of what they make. Taylor employees are given the first dibs the day before the sale, so the really interesting items are usually gone by Saturday morning. Nice employee benefit, eh?
The tour, on the other hand, is only done during weekdays, starting at 1 o'clock sharp. You'll spend about 90 minutes on a guided tour, which touches many areas of the shop. I haven't been on the tour in a few years, so I can't comment on exactly what's in the "company store" (as you say it) but I doubt the selection is anywhere near as vast.
I would say it's entirely feasible to, if they hold a public sale in 2012, take the Tour on a Friday, enjoy some great Mexican food, then Saturday morning sample the sale. (The last two have been public, but in earlier years you had to have an invite. I guess Taylor's circle of friends just keeps growing!)