Chris Torek said he has been studying Git's configuration handling in detail, covering both "git config" and the implicit changes made by commands such as "git branch" and "git remote". He described no serious bug. He did flag an edge case that appears when a user manually edits .git/config to add include directives, for example by taking [remote] or [branch] sections out into a separate file.
brian m. carlson replied that includes in .git/config are used in some cases at his workplace and that his colleagues want them to keep working. He does not know exactly why they do it. He said their fork of Git has a checksum covering the config file, but not included files, that must stay in sync across replicas. They may be using includes to try a setting on one host during development.
He added that other people might want this for other reasons, one being personal configuration, so Git probably should not break it even if it looks odd.
The excerpts show no other replies and no proposed patch.