I agree with your analogy, but for a large team, you can't ignore the 'broken window theory' [1] as it applies to code quality. If the codebase is messy and inconsistent, even in those 'hidden' files, developers are going to be less inclined to implement their new feature(s) with any consistency or quality. "I'll just hack this thing in here, since we really need to rewrite this entire module anyway; we'll clean it up then..."
[1] https://en.wikipedia.org/wiki/Broken_windows_theory