Update documentation to match Praefect's new configuration structure

See merge request https://gitlab.com/gitlab-org/gitlab/-/merge_requests/110379



Merged-by: Toon Claes <toon@gitlab.com>
Approved-by: Evan Read <eread@gitlab.com>
Approved-by: Grant Young <gyoung@gitlab.com>
Approved-by: Toon Claes <toon@gitlab.com>
Approved-by: Patrick Steinhardt <psteinhardt@gitlab.com>
Reviewed-by: Patrick Steinhardt <psteinhardt@gitlab.com>
Reviewed-by: Evan Read <eread@gitlab.com>
Reviewed-by: Mark Wood <mwood@gitlab.com>
Reviewed-by: Sami Hiltunen <shiltunen@gitlab.com>
Co-authored-by: Sami Hiltunen <shiltunen@gitlab.com>