I'm not sure this is typically done at the sub-$1000 prices but most bike companies (especially the smaller ones) sell frame + bike-kit. You pick the frame and fork and then a base build-kit. You can then substitute some parts from the build-kit at a small incrimental cost or sometimes at-cost. The process is usually handled through an authorised dealer. This is how I purchased my Aegis. The cost between sticking with the pre-spec'ed kit and a custom component selection was not much more than the price difference of the individual components that were swapped. I still got to take advantage of the pre-bundling savings for those parts I did not swap.