Hello,
because sitemap generated for domain.com includes ONLY the pages linked to domain.com/.. and sitemap generated for [ External links are visible to logged in users only ] includes ONLY the pages linked to [ External links are visible to logged in users only ]..
So, if you have link like <a href="[ External links are visible to logged in users only ]">x</a>, it will be included in one sitemap, but not in another.