Natural != how the machine works. Few of us have the faintest clue about how the laws of thermodynamics apply to the internal combustion engine or how solid state physics leads to semiconductors leads to electronics leads to electronic injection. Yet we all drive cars as naturally as we walk.

I'd argue that your analogy strengthens my point. In their original form, cars involved people manipulating the mechanical parts as directly as possible (the steering wheel was completely tied to the front axle, the gas pedal, brake, starting crank all directly controlled a single aspect). And yet, we drive cars so naturally. I think using the word natural in this sense makes a lot of sense.