But what I'm saying is that the formatting of a file may contain contextual clues that will help someone reading the code to understand what it does. Formatting isn't just chrome around the code.

Example: In Java, when writing a custom predicate to filter by foos that are bars, I prefer

        filter(myList, new Predicate<Foo>() {
            @Override public boolean apply(Foo foo) { return foo.isBar(); } });

        filter(myList, new Predicate<Foo>() {
            @Override
            public boolean apply(Foo foo) {
                return foo.isBar();
            }
        });

especially when there are multiple of them and they line up neatly underneath each other.

Any meaningful autoformatter would change the latter to the former, and in the process loose readability.

EDIT: Another example would be when using the builder pattern - getting those methods to line up to be neatly readable often takes some none-standard indentation.