For machine built wheels, it really depends on what you mean by machine built, if a generic pair of wheels, as seen on a low to mid end bikes, then hand build will always be better, if you mean machine built by big brands, like Fulcrum, Shimano, Reynolds, Zipp etc, these will have been computer designed, and should be perfect straight out the box, and will be as good if not better than many hand built wheels.

In your case, the handbuilt option would be better than a low end machine built set