They are institutes, not universities.

Could you elaborate a bit? What sort of "non-universitiness" is it that makes their absolute best in the world research and teaching rank 5-9 spots lower than their success would dictate?

Because this was the list of top universities, not of every possible institution. MIPT for instance, once of the top physics powerhouses is absent as well.

A university has a wide scope of taught subjects and substantial variety of curriculum, which makes them a separate category in academic world. And the list was of that particular category, that's it.