I never used MooTools selectors, problem is with GSAP selectors while using it with MooTools. To prove my point check my last code where I use jQuery selector and code works fine, removed $() to get rid of jQuery selectors and GSAP fails(in presence of MooTools). Remove jQuery to use GSAP with MooTools only and GSAP selectors will fail(take a look at my first codepen).
I don't know if MooTools is doing it wrong or GSAP, neither is problem of Joomla because above code is single HTML file with similar behavior. My knowledge isn't that deep but I guess when we declare noConflict before MooTools, it takes control of more than just $ sign and affects GSAP in the process. GSAP developers should look into it.
Finally if anybody comes to this thread with same problem, I will recommend to use jQuery selectors. Thank you.