Wouldn't it being hidden make it much more attractive? You can put junk it in and users won't complain, and if they do want it you have a help article on your site.
I remember asking a games porter (from Windows to Mac) once why they put savefiles in the Documents folder instead of Library (some older games of theirs did put them there) they replied that because after Mac OS X changed the Library folder to be invisible they had people contacting support being unable to find the savefiles, so they put it in a place where it was visible.
I'd expect the "less attractive" part is for when you do want users to find the data your program creates in general.
That's an interesting use case. I guess there's a class of users who are smart enough to want to manually copy/backup files but not smart enough to know about hidden folders or standard directories. Windows has a similar situation with its hidden AppData directory, and Unix with its hidden dotfiles.
I hadn't given this much thought but now I am disappointed that the people who came up with these standards didn't do more UX research and trial & error with actual users. Perhaps if they paid attention to all the use cases and stakeholder needs it wouldn't be such a mess.
No, because part of the point of all of this is “how do I move my config to other computers, or manage it across multiple computers at once?” Hidden “junk” gets lost, is hard to support, etc.