When using the wizard to create a node template, it adds the comments and comment form underneath the content in the panel editor. That does make good sense to replicate a normal node display.
There are some problems here with the permissions or something though.
I've noticed that when comments are disabled via the node, the Comments title and login links are still displayed for anonymous users, even without the permission for anonymous users to post comments.
For any logged in users things seem to work correctly, and comments and forms are not rendered.
EDIT: Using Omega theme, I'm aware it does some things differently, so thought it could be worth a mention...