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
3) When asked, "Native apps that use the browser control, will they have access to this?" Answer: "any javascript rendered though the os will be enable for webgl", not sure if that was the answer i wanted, but take it as you will.
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.