Although you can't build the motherboard, power supply and case (you have to buy them as a set -- as a whole computer), you can augment the unit once it arrives by adding additional hard drives, optical drives, memory, PCI cards, etc. from other manufacturers to expand the storage/RAM/capabilities. Depending on the unit, you can even upgrade the processor (using processor upgrade cards or PDS slot capabilities in various macs).
In theory, you could order just a motherboard from a repair channel (or eBay) and build the rest of the system from the ground up, although you would be unlikely to find the newest generation of motherboards & processors readily on tap to buy through an apple channel.
And although you can build a computer equally configured as a current MacPro tower for about the same price, finding a competitor's pre-built product with the same configuration will normally be more expensive (I priced some equally configured Dell's just a few weeks ago).
But Apple has a computer for the penny pincher in you (that makes you want to build from scratch) already: the MiniMacs.
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On a separate note, I've noticed that Apple's store staff at a couple stores I've visited have definitely taken a nose-dive compared to how they were when they first opened. Although I could understand it during the Christmas-season rush, even yesterday (31 Jan) they were far less than optimal for any store in any trade that sells high-end goods. The genius bar wasn't stocked with geniuses, and several of the employees were patentedly rude compared to what the corporate policy is...
Sidenote: my 30" LCD display was going back in again for repair, this time with a preset 3rd-tier case issue number tied to the video engineering department at Apple, because the first time it went in, they didn't do any repairs -- sporatic problem with black jittering to red. Staff at the store literally argued that I couldn't submit the unit without an appointment and their genius' diagnostics skills; I was already annoyed that I couldn't ship the unit directly in and instead had to heft it down to a store half a county away.
Cheers,
=-= The CyberPoet