Even though Apple charges list price for components, the company lets you swap out features and doesn't charge you for installation. Since you can't substitute or swap pre-installed components to get better ones, you'll have duplicates of several of those features you upgraded. And that costs extra money. An obvious example involves upgrading to 100BaseT Ethernet. Since all personality cards in G3 Macs include 10BaseT Ethernet, you'll need to buy a new 100BaseT Ethernet card.
Further limitations prohibit resellers from installing particular components.
The result is that, if you don't buy directly from Apple, prices increase, expandability is limited, and installation fees add up. This would let resellers configure the systems in order to substitute and remove components if necessary, which in turn should let resellers' prices match or beat Apple's. But Apple's offerings are limited, because the company can't take advantage of the plethora of manufacturers making computer components. Just imagine, all these options . . . But now you're left with only one free PCI slot.