javascript - window as prototype makes setTimeout behave oddly

Question

This question is related to my previous question (using window as a prototype returns seemingly wrong values in javascript) which was answered by @Stubb0rn, but I faced another problem:

function W(){
    var w=this;
    Object.defineProperty(this,'window',{configurable:true,enumerable:true,writable:false,value:w});
}
W.prototype=window;
window.setTimeout(function(){console.log("123")});     // works ok
(new W()).setTimeout(function(){console.log("123")});  // throws Uncaught TypeError: Illegal invocation(…)

please note I am using chrome to test

Answer 1

Resolved it, it turns native functions needs to be called from within window context so I ended binding the functions in window and doing double prototyping like what follows:

function define(w){ // for testing I use requirejs define instead
    window.Test123=w;
}
(function(){
    function WBase(){
        for(var i in window){
            if(typeof window[i]=='function'){
                this[i]=window[i].bind(window);
            }
        }
    }
    WBase.prototype=window;
    function W(){
        var w=this;
        Object.defineProperty(this,'window',{configurable:true,enumerable:true,writable:false,value:w});
    }
    W.prototype=new WBase();
    define(function(){
        var windowAlias=new W();
        return (function(window){
            var ret={}; // returns only the variables added to the alias window object
            with(window){

                // CODE FROM MODULE HERE WILL HAVE an alias to "window" wich means if it adds variables to window (global scope) it will be prevented and instead added to the alias window

                for(var i in window){
                    if(window.hasOwnProperty(i)&&i!='window')
                        ret[i]=window[i];
                }
            }
            return ret;
        }).call(windowAlias,windowAlias)
    });
})();

Test123();  // for testing

try pasting jquery in place of comment (// CODE FROM MODULE HERE...), you'll get an object with properties jQuery and $ and they will not be added to the global scope. and I ended up creating a page that appends these lines dynamically for javascript files requested through querystring