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.
It's a native application, but it's still interpreting JavaScript as far as I understand it. In a test I did a while ago, I seem to recall cocoonjs being less than half the speed at running code than safari on iOS, so being a native app isn't helping it there (I haven't tried the new 1.4 version though, maybe it's improved).
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).
But what results in 60 fps is highly variable. I can get 60 fps out of cocoonjs 1.3, but 1.4 with webgl is faster at rendering, so developers can do more per frame. A blank white screen is easy to process, but tons of collisions, instances and code running at once might get 60 fps in safari but not in cocoonjs. If JavaScript was replaced by something faster, it would be a significant boost to what people could do.
Node-webkit exports as binary to desktop and so has about the same performances as chrome on desktop, so no issue/relevance there either.
It's still relevant from a technical perspective, because node webkit is also still running JavaScript to run the C2 games. Even if v8 compiles them, as the article states, they can only do so much. However, it's true that the article is mainly talking about mobile, and desktops are fast enough that the concerns aren't really an issue, even on my amd Athlon 4400+ which scores like a tenth or less of the speed of a lot of modern processors.
My biggest frustration is that no one seems to be willing to collaborate on a proper modern language that solves all of the problems that JavaScript has. Nacl/pnacl sound brilliant, but no one else seems to have any interest in it. Dart also solves a bunch of problems, no one else seems to be backing that either. Everyone keeps talking about web technologies being the future but they keep using a language that is stuck in the past that simply has a lot of inherent performance problems, as it simply wasn't designed to be a high performance language. What we end up with is the equivalent of people trying to put rockets on a clunker to make it go faster rather than properly design an F1. Even if you can make it somewhat fast in the straightaways, the sucker can't turn.
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.
Edit: ninja'd