How to theme separately the node content and the comments
A- The node_menu (hook_menu implementation) has node_page_view() as a page callback for a node page.
B- node_page_view() calls node_show() which:
1- is not a themable function.
2- mixes (concatenates) the output of node_view() (the node content itself) and of comment_render().
C- comment_render() calls theme('comment_wrapper', ...)

This is where the serpent bit its tail:
As mentioned in the question, I could reimplement comment-wrapper.tpl.php to nix the output mixed with the node,
but then calling comment_render() separately to get the comments where I want returns nothing for the same reason! 

The conclusion is that the solution cannot be implemented by a theme alone. One would need to implement this in a module and override the node_page_view() callback and re-implement node_show(), taking care of the fact that node_show() is also called when viewing a node revision ('node/$nid/revisions/$vid/view').