If you're buying new parts, you'll likely pay more by building up from the frame. Two reasons...

1) When you buy the entire bike from the manufacturer, they're able to cut component prices by buying in bulk. You might be able to scour the internet/ebay and eventually find what you need at bargain prices, but the question you'll have to answer is whether it's worth your time.

2) You're likely to get the upgrade bug as you go.

With that said, there is a lot of benefit from building from the frame up, namely, you get the bike you've designed and spec'ed. If you're not going to be satisfied with the components delivered on the complete, by all means, go for the build or get your LBS to do it for you.