I think there is a lot of confusion about what is really CocoonJs .
CocoonJS (Canvas+) is not a browser, it's a wrapper that mimics a browser intercepting draw calls and "converting" them to OpenGL ES calls so you can't expect the same behaviors that you can see using a real browser.
"WebGL is faster than Canvas2d" is a true statement only when there's a real browser involved but since WebGL is not supported by iOs what we see on our iphones screen is an "emulation".
Ashley said once that WebGL engine is a little slower due to technical reasons on javascript execution side and a lot faster at drawing things on screen. So, in the end, you have an huge performance improvement. But this happens only on real browsers.
We don't know how CocoonJS works behind the scene but we know that the iOS SDK agreement requires apps to use Apple's own JavaScript engine which is a lot slower than modern JS engines.
My speculation is that since maybe CocoonJS accelerates in the same manner both Canvas2d and WebGL calls, the gap you see in favour of Canvas2d is related to the slow and old JS engine that apple imposes on their developers.