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For the same reason a modern CPU has capabilities far beyond what's exposed through Javascript or Ruby: it's easier to build a simple general purpose device and then implement any API through a software layer than to make hardware implementation of every complex API.

I would think future updates to OpenGL/DX could allow more features of the cards to be used by devs. Otherwise, to use all the features of a card, the game would need to be heavily optimised which increases development time and costs, and then only supports a certain configuration which would be such a small amount of people that all that development wouldn't be worth it.

Many of these features are no doubt used by the driver author(s) to implement cool stuff in GL extensions. One particularly crazy example: https://developer.nvidia.com/nv-path-rendering

It's not because of opengl or directx, it's because of the operating system layer.