The "tendency of CLI applications to do it wrong" comes from the fact that they are following the *older* unix (de-facto) standard, which is to put config files in the home directory as dot files.  That is, they are *not* doing it wrong, they are following the older unix de-facto standard and not the freedesktop.org standard (which, you will note, is a standard arising out of GUI applications, not CLI applications).

Not, mind, you, that I think .config is a bad standard, I'm just saying that if you want to follow standards you need to account for the legacy standard as well as the new standard.