It seems Stencyl guys solved the problem in Stencyl 3.0 by rewriting the entire engine in Haxe. With it they get Windows, Mac, Linux, Flash, iOS, Android, HTML5, and more. All native. Not sure about performance , yet i've seen mentions of it performing very well in iOS. In Windows it generates C++, so native code. This is 'confidential' info btw. Only know it because i ocasionally lurk at their forum.
This is Ejecta , it appears, is just a simplified CocoonJS like tailored to be used with ImpactJS engine.