Yes, what you said is exactly what I did. The shop had the frame I wanted, with different components. I took the cassettes and cranks off of my old bike, they ordered me the R700 brifters, and I bought the bars for them to put on.
Of course my bike is a more "boutique" brand, but it was not more expensive than some of the Treks you are looking at.
They wanted me to be a happy customer...