Most GUI tools execute git under their hood, so if the repo config is set, they might pick it up.

Yes, but they sometimes have their own private copy of the git executables that can be out of date or with their own peculiarities, such as using their own git-config that the default command-line git in your PATH won't be using.

Not all? I'd find it scary to use a tool that makes its own things not relying on Git