What you're glossing over here is that about 10-15% of the timber you buy to frame a site-built house is wasted (ad-hoc cuts, bracing, jigs, etc.) and thrown into a dumpster.
If a house is pre-planned, you can use a machine that cuts each board to length, and join the ends of each board using basic joinery processes that aren't practical when building a site-built home. You can pre-fabricate things like trusses and wall segments so you (or your workers) aren't driving 100k fasteners to fabricate something a robot could build in 1/10th the time.