Well that really is the explination. Through the speed force mostly all physics are negated. How on earth could his body heal faster than its being deteriorated by the sheer force of the speed? Yeah he can heal, but at those speeds you're healing power would have to be faster than the speed he can travel. So instead, the speed force I.e. magic. Allows him to travel time, withstand those speeds, comprehend them, react, etc. With that factor I could see it being plausible for him to strive throuvh the molecules Good observation though seriously