Update gitaly config to not use duplicate storage dirs

What does this MR do and why?

While the current configuration does work, it's not considered a correct configuration, and is something that is planned to be deprecated in a future release. Let's update the config here to reflect to more 'correct' configuration'

Closes Stop using duplicate storages in Gitaly's confi... (#719 - closed)

How to set up and validate locally

The easiest way to verify this is probably via GitalyCluster which verifies that config continues to work.

• bundle exec exe/gitlab-qa Test::Integration::GitalyCluster EE --no-tests can run the the configuration and allow you to interact with the setup locally.
  The tests likely to be impacted by this change are those in the GitalyCluster and Praefect jobs so we can review those jobs as well.

MR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

• Commits include Changelog: trailer
• I have evaluated the MR acceptance checklist for this MR.