AFAIK, if the bike is brand new, you simply pay the difference - they use the components elsewhere. If you ride it for a bit then upgrade, you pay the whole cost of the new component. That's how it was explained to me at my LBS, in terms of a chainring, anyway.
On the other hand, the more you ride the bike, the more you will know whether you need to make that change, and what to change it to.
In any case, check with them first.
Steve