So I talked to one of the product managers of IE, the guy who was running the WebGL talk.
WebGL is being baked into windows at a low level. Couple of things.
1) WebGL is not native, they are doing a translation from WebGL -> DirectX11 on the fly. No perf hit because WebGL is so simple.
2) All versions of IE11 will be enabled for WebGL, tablets, etc
Also, it seemed pretty clear they are using three.js as the base for the api. So, they will support WebGL calls that three.js calls first.