Maybe there is a module_setting to put it on TOP of the body or on the BOTTOM. But most modules just append. When displaying the node, all of that comes into $content in node.tpl.php. So if you want to configure that, you have to redo the whole body yourself. Then, if you install another module that adds to the node body through hook_nodeapi you have to go manually add that to your node.tpl.php for each one.
If we constructed it like FAPI, with weights, etc. We could allow modifications of that right before calling render_body($node) or whatever. So hook_nodeapi('view') could do something like
i think most people agree that the fapi array model should extend beyond forms to viewing as well. i don't think we have much idea yet for how to do this though. there are many more examples beyond $node render, so lets be broad in our thinking.