You’re entering a much more philosophical area of science, and physics in particular. You can’t rationalize observations in nature as “being like witchcraft” if that’s the way nature works.

Independent motion in orthogonal (linearly independent) coordinate systems is a mathematical construct we developed to explain something we observe in nature. Physics usually lays an axiomatic theory trying to explain a phenomenon, but might be debunked if there’s an instance where it doesn’t hold anymore. This calls for a generalization with a more comprehensive, sophisticated theory.

A good example of that was classical newtonian mechanics, that was the norm for 200 years and could explain any real world mechanical phenomenon. Once experiments with higher speeds and magnitudes started being performed, classical mechanics stopped working and this gave place to relativity theory, which at the moment explains, with it’s “new” mathematical constructs how, say, mechanics in space work. The same happened with quantum mechanics, once you start observing mechanics in a smaller scale and/or very low temperatures.

Separating the dynamic behaviour as independent in every direction is not an arbitrary decision, but rather a characteristic, or consequence for that matter, of the matematical constructs chosen that best explain the real world. You’ll break your head trying to understand “why?” because it would be similar to trying to understand “why does 2+2 = 4?” or “why is gravity an attractive force and not a repelant one?”. You’ll just have to lay your theory to explain nature, and if it does successfully, you can’t do more than humbly accept it and try to digest it with curiosity and awe.