I would like to "hide" Certain Pages or entries from the Content SEO Section as they are never seen by the end user and are not used in the XML sitemap. Is there a way to do this ?
A Section only appear in Content SEO if it has public URLs. If it has public URLs, that means that Google and users will be able to find it eventually.
There is a setting to disable the sitemap for a section via Content SEO, however.
Can you elaborate on what you're trying to accomplish?
Also we got into detail on sitemaps for a while on the devMode.fm episode SEO for Web Developers: The Silence of the Chickens which might be useful to you.