Yes from very start I never used $ symbol and out of all the different ways I tried to get to the root of the problem, only disabling noConflict in plugin which stops that single line file from loading worked for me, which makes me believe is the problem. And while I was typing I tested it locally as I am not sure if I can edit codepen this way, here is code that confirms noConflict before MooTools affects GSAP.
<!DOCTYPE html>
<html>
<head>
<title>GSAP n Mootools</title>
<style>
div{
display: block;
position: relative;
height: 100px;
width: 100px;
background-color: #234455;
margin: 10px;
}
</style>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
<script>jQuery.noConflict();</script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mootools/1.5.1/mootools-core-full-compat.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/gsap/1.16.1/TweenMax.min.js"></script>
<script>
jQuery.noConflict();
(function($){
$(function(){
$("#one").click(function(){
TweenMax.to(this, 1, {left: "+=100"});
});
$("#two").click(function(){
TweenMax.staggerTo("div", 1, {left: "+=100"}, 0.2);
});
});
})(jQuery);
</script>
</head>
<body>
<div id="one">
</div>
<div id="two">
</div>
<div id="three" >
</div>
</body>
</html>