For Git clients in particular, there's the issue of GUI applications that think their mostly ad hoc, incomplete configuration should prevail over standard Git

For Git clients in particular, there's the issue of GUI applications that think their mostly ad hoc, incomplete configuration should prevail over standard Git configuration (e.g. GitAhead is unable to use authentication tokens on Windows) or that their "opinionated" behaviour is good for everyone (e.g. try to modify a tag with SourceTree).