Allow Geo secondaries to have custom git user config... for now

https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/13930 introduced a custom git user config check that will cause rake gitlab:check to always fail on secondaries.

We should update the check so it permits custom configuration on Geo secondaries, since we currently depend on this for SSH mirroring between secondaries and primaries.

The documentation will also need to be updated so that we don't create custom config on primaries, and so the DR promotion instructions take out the custom config too.