Hi @kirthi,
The goal of packaging Mattermost with GitLab was to make Mattermost easy to install.
If this is not the case, I'd propose installing Mattermost separately using step-by-step instructions and then configuring GitLab-Mattermost SSO integration directly.
Once it's installed, Mattermost is just on binary file to replace on upgrade, and setting everything up cleanly makes everything simple to administer while keeping all the benefits of GitLab integration.
Does this help?