For the kind of money these bikes command, I would not hesitate to ask for certain accommodations. Co-Motion inevitably falls under the category of "high-end custom" bikes. These builders generally use the standard build as a guideline for those who have the bucks for a high-end bike, but don't know much about their exact needs (customization.) For you, however, they should build a bike according to YOUR specs for 100% satisfaction. I can't imagine them not accomodating you. A common scenario is allowing to you ship to them (or maybe they can special order?) the few different components you need on the bike and crediting for the ones you don't use from their standard build. This could apply to things like crankset, cassette and saddle, for example. I bet they will oblige if you ask.

BTW, as far as the FSA crankset, save your money. I believe reading reviews that anything from Shimano (Deore and up) will just perform better.