Yes of course, the options for ghost install are documented here:
https://docs.ghost.org/docs/cli-install#section-options
The CLI will create entirely new, separate files, as per the templates I linked to above & then will symlink those into place in /etc/nginx/sites-enabled/. No existing files will be touched.
If there is some configuration elsewhere in your nginx config that “trumps” or conflicts with the Ghost config, it could definitely still cause trouble. Undoing that would be a case of removing the added symlinks and restarting nginx. Our templates deliberately do not use the default_server directive, which reduces most opportunity for conflict.