I think you are missing one point: mental load. I doubt people keep all their files in one directory or all their emails in one folder or just have one large drawer with every possible kitchen utensil in a pile. The same is true for code. Organizing your code around some logical divisions allows for thunking. I will agree that some people take it too far and focus too much on "perfect". But even some rudimentary directories to separate "areas" of code can save a lot of unnecessary mental gymnastics.