Godot is following the linux convention.
The ".config"-subfolder contains small config files of different applications but no user files. If you intend to store actual data creating a folder the way Godot does is the way to go.
I mean right now I have in my home folder subfolders like ".steam", ".adobe", ".dropbox", ".kde", ".gnome", ".java", ".thunderbird"... if those companies decide not to put their user folders inside the .config-folder you should probably follow their lead.