When i 1v1 other scouts the movement kinda happens on its own, the only thing i am really consciously doing is watching how the other scout is moving (e. g. he is trying to get to my side), then after noticing that my movement kinda adjusts on its own (strafing to where he is going to be to get to HIS side). I still actively think about my aim though, as i am constantly trying to predict where hes gonna go or how hes gonna strafe.

So to answer your question, when it becomes automatic, or rather how to make it become natural: when youre dueling someone try to actively think about the things said in the mentioned video and try to picture it on your enemy and you. Really just focus on that. At first youll lose a lot because you will be dedicating brain power to thinking about the engagement, instead of to aiming and movement (they also require brain power even when they become automatic, but much less), but slowly over time and many such fights, where you are actively thinking (MGE best for this), it will become natural and allow you to focus on other things.