You are right, there is something more fundamental to strive for: purpose. Alignment, whitespace, hierarchy and contrast are elements of visual syntax. You internalize the rules so much that when you’re designing you’re not thinking about it; you are thinking about what you are trying to achieve.

Say you need to design a sign-up page for a newsletter, you need to:

  1. Tell users what the newsletter is about

  2. Say how often it’s published

  3. Make them feel comfortable giving out their e-mail

  4. Give some demonstration of value

As you are designing, you are thinking about what is the best way to accomplish each of these goals in a visual manner. You often don’t even think where to align stuff, it just falls into place because you know where it’s supposed to be.

If I were to make a parallel to code, it would be clearly internalizing the syntax of the language. You no longer think about where to indent your code, or of a comparison operator in javascript is == instead of =, you have achieved enough fluency to stop thinking about how to write code and actually achieving something.