Stop using duplicate storages in Gitaly's configuration

As per Stop supporting duplicate storages in Gitaly's ... (gitaly#5598 - closed) the configuration for gitaly is planned to be updated to not support duplicate storages in Gitaly's configuration. This will cause our current setup in Gitaly to break due to the configuration in https://gitlab.com/gitlab-org/gitlab-qa/-/blob/41fdc5fe2db3063072b215a4a322f7d362f413f4/lib/gitlab/qa/component/gitaly.rb#L75-83

We need to update this configuration to avoid using duplicate paths.

Additional context: gitaly#5664 (comment 1786289905)