So I recently discovered that Studio is using ANGLE for shaders. More information can be found on Google code.
http://code.google.com/p/angleproject/ANGLE basically lets you use GLSL/GLES shaders in Direct3D. It is used in Google Chrome and Firefox.
As you can see Studio is using it.
Now I was originally spouting nonsense about CG which is even more proprietary than HLSL and just as bad. This may actually be one of the few things YoYoGames did correctly. However it is important to note that this project is BSD licensed and I am not sure if we could make it optional if implemented.
I also discovered that Studio does not mention them in the licenses tab of the launch section like they do Box2D and other things. This either means they made a mistake and are inadvertently or purposefully infringing the copyright, or they have some sort of deal with Google.
However I am still missing something fundamental here I think, because the following page suggests that ANGLE also abstracts vertex/index buffers.
http://code.google.com/p/angleproject/wiki/BufferImplementationThis could explain why Studio does not allow you to choose the graphics system because it only has 1 graphics system, in theory, but I have no evidence.