The clash between the timing of CSS transitions and the fade effects of jQuery

Check out this link: https://jsfiddle.net/nsx6nvs5/

Here is the HTML code:

<div id="btn"></div>

This is the corresponding CSS:

#btn {
        height: 100px;
        background-color: red;
        transition-duration:1s;
    }

        #btn:hover {
            background-color: green;
        }

And finally, we have the script:

$(document).ready(function () {
    $("#btn").click(function () {
         $("#btn").fadeOut(2000);
         setTimeout(function () {
             $("#btn").fadeIn(2000);
         }, 3000);
     });
});

There seems to be an issue with the fading effect. Why does fade conflict with transition-duration?

Note: The click event is not the problem. It occurs with other events as well!

I have researched this and it seems like this question has been asked before in a different scenario but remains unanswered.

Conflict between CSS transition and jQuery fade

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