For the question about commenting, that could probably be modified in the plugin. Generally, plugins add their functionality to a page with a hook in plugin.php. You could modify the code there to check if an item is in a collection that should allow commenting, and display it accordingly.
Only displaying tags based on collections would be more complicated and might be best in a separate plugin, but could follow the same principle -- you would check to see if the items that have the tag are in particular collections. That's doable, but might take a little more work