Some settings for components managed as part of GitLab’s omnibus install can be configured in /etc/gitlab/gitlab.rb They have been slowly adding more and more support for advanced configurations. See this doc for more information on how to configure Nginx settings through it.

The simplest way to do what you are after is probably to add a custom include directive. This will allow you to set up a separate Nginx config file for “website.io” In /etc/gitlab/gitlab.rb add:

external_url "http://git.website.io"
nginx['custom_nginx_config'] = "include /etc/nginx/conf.d/*.conf;"

You can now create a server block for your main site in the /etc/nginx/conf.d/ directory. Then run gitlab-ctl reconfigure to pick up the changes.

You can also disable the bundled Nginx all together and install the distro version if you want by adding:

nginx['enable'] = false