They don't actually manufacture any of it. OEM/ODM suppliers are used for every part in systems, custom or not. They assemble, locate/produce drivers, and test the system before it goes into mass production (assembly of finished components & packaging).One of the reasons they up-charge that way is that their isn't a whole lot of profit to be made in upgrades. There is no reason for them to cut their margins on ram, HDD's etc, because they don't manufacture those items.
They don't want the overhead associated with owning/operating manufacturing facilities. (Components through finished boards).