The omnibus package is similar to the nixos way of things, except focused on one application rather than the whole system. Once the package is installed, it uses a configuration file, and a set of Chef cookbooks/recipes[0] to configure the individual components.
So yes, Gitaly does come with it's own configuration file that needs to be managed. It does use the same paths as the main gitlab-rails application, so our cookbook has a method to convert the configuration of one to the other[1]