I've never had trouble ordering what I wanted from the options list. That usually means needing to pay more, though.

If you want custom leather seats, you can drive your car off the lot into one of many shops that offer such services, or other customizations. Me, I drove to the stereo shop to put a better stereo in (back when the factory ones were terrible).

There are many reality shows on TV featuring shops what will custom build a car to your specifications.