This is true, it would cost less to have 100,000 of one single part than it would to have 10,000. However, when dealing with wiring harnesses and the different options available for each model it creates a different story. If an S, Se, Titanium, and ST all had the same wiring than everybody would have connections for heated seats, fog lights, rear 12v outlet, connections for both a 4" screen 8" screen, rear view camera, audio controls on the steering wheel, 6 speakers, etc. This would allow a person with an S model to upgrade to a titanium simply by plug and play from wrecked cars or aftermarket parts.
It makes sense when you realize how complicated the harnesses are, plus it means vehicles can be reconfigured late in production or even after delivery.