I don't understand this.If you order any phone from the Apple Store for in-store pickup,they HAVE that phone.I have never heard of anyone ordering and being turned away in the time I have been here.
3 separate people in store told me they did not have 32 GB gold for AT&T, despite their website showing otherwise. I asked them what would happen if I completed the order online. They said that stock isn't confirmed until you receive your email, telling you that they're ready for you. They said it could take days to receive that email if they don't have the product in stock.
So I guess my advice would be to use the website's availability indicator as a guideline, but don't count on it being accurate.