The CPUs are soldered to the board, so BTO CPUs have to be built-in from the beginning. They probably have a bunch of boards with the 3.06 or whatever chip sitting around. They probably have a separate BTO assembly line. When someone orders a 3.06 with a RAM upgrade and a HD upgrade, they assemble one computer with those specs and ship it out. It would be extra work for them to assemble a computer, then take it apart, upgrade it, and put it back together. They might as well just build it BTO from the start.
If someone orders say, a stock processor with a RAM or HD upgrade, they probably either pull the computer off the main assembly line before those components are added, or just build them on the BTO line.
It only makes sense to ship BTO computers direct from the factory because that is expensive. For the stock configurations, they put a bunch of them in a container, which travels for a few weeks on a boat to a distribution center somewhere in the US or Europe, where they are then sent out to Apple stores and online customers. That is not acceptable for BTOs, though, since people don't want to wait weeks for shipping.
I haven't seen Apple's (or Foxconn or Asus or whoever is making MBPs these days) factory, but what I described is likely the cheapest, thus the best way to do things. If Apple only got a few BTO orders, taking apart an existing computer might work (except for the CPU), but think they get enough BTO orders that that doesn't make sense for them. The BTO assembly line could be less automated than the main assembly line, though. For example, if they have a memory installing robot on the main line, they might just have a memory installing person on the BTO line since a second robot would be expensive.
