What is your Kindle's Sort Order set to? It should be "Collections", but any other sort order will list both the books and the collections.
Collections sort will only list collections + books that aren't in collections. It doesn't require any hacks or non-Amazon tools at all.
As for listing books in the order they were added to the Kindle, that information is not stored anywhere on the Kindle.
"Collections" or "Recent" will both sort by the order they were last opened, though.
This is on the *Kindle*, not in calibre.