This is pretty infuriating to me. There isn't a consistency as to where things are stored. Isn't all that stuff (like .conda and .cache and .viminfo) supposed to be in AppData\Roaming? Almost nothing on that list (save for the default folders like Desktop and Videos and AppData) should really be there. Why is it still there, and is there a way to prevent programs from doing this?
You'll need to talk to the program authors. They are the ones who decide where to save files be default in that location. Most of those are due to programs that are cross-platform, as *nix systems use . at the start of a file/folder name to indicate a hidden attribute.
More info in my answer
There is almost no Windows' programs in your screenshot.
Why do you think non Windows' programs would follow Windows' rules.
Programming in Windows is a skill.
There are multiple generations of requirements as to where to store files etc. I program to Windows 2000 standards.
User interface guidelines are also multiple generations. Again I program to IBM's Common User Interface which is the basis of 16 bit and Win 9.x user interface standards (like notepad).
Todays practise is to be mobile app like for consumer programs.
So you can program cross platform and be mediocre or specialise in a platform and write great apps or traditional applications.
See https://docs.microsoft.com/en-us/previous-versions/ms954115(v=msdn.10)
