Well, they are supposed to be all in .config, problem is many app developers think they are special little boys that deserve its own directory
It all sounds so easy, until you learn about the XDG Base Directory Specification[1]. You're actually supposed to do a whole song and dance around a hierarchical set of environment variables, associated defaults, and resolution orders.
Interfacing with people is never easy.
%LOCALAPPDATA% on Windows. Or better still, use GetAppContainerFolderPath or SHGetKnownFolderPath with FOLDERID_LocalAppData.