I found out that go-git is unable to parse a config with a multi-line value, like so:

[alias]
    myalias = "!f(){ \
        echo hello; \
        };f"

This is however explicitely valid as per https://git-scm.com/docs/git-config#_syntax

go-git/gcfg#1 and go-git/gcfg#2 address this issue.