Why is research at highly productive research institutions better than those at not-so-highly productive research institutions?
Your question is a bit circular. The "best" universities are at the top of the list because it's a list of the "best" universities -- however that is defined. :)

What makes a "top" university is largely a rich-get-richer feedback loop: The "best" universities attract the "best" researchers, which makes them the "best" universities. The "best" researchers get the most funding, which helps them do the "best" research. The "best" universities get the most money, which helps them spend more on research.

That explains why older universities tend to have higher rankings. They have had a long time to gradually build up that feedback loop. However, external factors have a big impact -- availability of funding and university management is important, as is the desirability of the location/country. Countries like the UK and US have a lot of good universities because they are attractive places to live and their government provides adequate research funding and, importantly, this has consistently been the case for decades or centuries.

One important point you are missing from your list: Some professors are teaching six courses per year -- they have no time for research. Other professors are only teaching one course per year -- they have plenty of time for research.