I have external diff and merge tools that I prefer to use configured in my git config. The tools I prefer to use are different depending on if I'm at the CLI or in a GUI such as SourceTree.

Nonetheless, SourceTree only allows me to change away from a default external tool iff it has permission to edit my global configuration files.

If a tool has been configured with the permissions enabled, then the permissions removed, SourceTree reverts to using the default.