You are missing the point. The kernel is still abstracting over those GPIO timings so programs don't need to know the timings themselves. This is the benefit of using a platform. These low level things get abstracted away from what you have to do.

Oh, I see. You're piecing together the layers much like a cake.

The way I see it, everything is tied together as some kind of flow chart where different elements have different jobs. Linux is quite a small part of the system when compared to Google Chrome. Even if you were to invert the cake, as a whole it still wouldn't make sense to me to see it that way.

Hardware tends to have more distinct layering than the lalala-land of software where pretty much anything goes.