Yes, that's what the data shows: The cost per paper is higher in large universities. You still have to question the data to be a good scientist, so we're trying to find the causes of all of that. I can't say that that's what it proves, but the data shows that it definitely costs more.
To put it charitably, we know that the big universities work extensively with the small ones. In all likelihood, it could be said that there are ripple effects on the smallest universities. More research is needed on the matter. It goes back to what my colleague said: We need data on the research system.
What we want to do in our labs is to find a way to fund it. Among other things, public policies should be created to fund research more fairly and generate the greatest collective benefits. For that to happen, the granting agencies have to share their data.