I haven't read all the article you've linked, but it just sounds like it's not talking about what C2 and cocoonJS really do.
You're not having a browser executing your JS code when exporting through cocoonJS, you're having some native application.
And even if it is "slower" as other apps, the recent cocoonJS 1.4 deals a solid 60 fps on most android devices (awaiting for Apple's approval on iOS) and that's what mostly matters as far as games go. (Also taking into account the recent addition/modification of 2DBox physics specifically for mobile through cocoonJS which should allow for proper physics handling which, so far, could be a bit of a bottleneck in mobile CPU performances).
Node-webkit exports as binary to desktop and so has about the same performances as chrome on desktop, so no issue/relevance there either.
Regardless, even on mobile, even in cocoonjs which is not as fast at running code as safari, it's obviously still fast enough to make a game with.
I'm not really meaning to complain about the performance issue either - it's fast enough for most of what I want to do on mobile, and desktop isn't an issue almost at all - I'm more frustrated by various groups' inability to work together to improve things properly.
Anyway, thanks for the article, Alcemon. It was an interesting read.