All the other builders besides the raw builder are cheaper when configured the same ways. The idea is that the S, V, etc. models are a package deal, and it entices you to buy more stuff.
For example, let's say I wanted a cheap 8887, with everything as low-grade as it gets, but I want 512 megs of ram. I might get a price of X dollars on the raw builder, but i might get the S model with the same specs but a faster processor for X + 30 dollars. Then I would think, "Hey, for 30 bucks, that's not a bad upgrade. I think I'll go that route".
Just like that, PC Torque makes a little more money, and you get a pretty good deal.

It's a pretty good system. Only use the raw builder if you want a really low-tech (relatively) machine--else, go for one of the package systems.
Brad