I haven't a clue what Apple actually stocks in the store, but I'll bet they keep the maxed out version of just about everything for the rare "I don't care what it costs the company is paying for it and we need it NOW!" crowd. A company the size of Apple can afford the inventory, especially given that their "top of the line" system doesn't change on a regular basis, and there are not that many versions of anything out there to sell. Apart from the consumer devices which they sell like hot cakes (iPod, iPhone, iPad etc) they have what, Two other product lines, a laptop and a desktop? That's two big boxes, maybe three with a monitor, so they got space.
Personally, I'd be surprised if they hadn't carried what you where looking for in stock. I'd be willing to bet that if you walked in asking for less than the top of the line configuration, you'd be sent to the website to order it. But when you have to have it *now* you can bet they are going to take advantage of that and be ready to sell you the highest priced system they can, which means the store only carries the top end configurations for buyers like you, plus a pile of consumer products to service the iPod/iPad crowd.