"It is true that all 3k+ authors do not draft the paper together, on the contrary, only a small part of them are involved in this very final step of a giant research work leading to a sound result. It is as well true that making the research performed public and disseminating the knowledge obtained is a crucial step of the whole project.
But what you probably missed is that this key stage would not be possible at all without a unique setup which was built and operated by profoundly more physicists and engineers than those who processed raw data and wrote a paper. Without that "hidden part of the iceberg" there would be no results at all. And it would be completely wrong to assume that the authors who did the data analysis and wrote the paper should be given the highest credit in the paper. It is very specific for the experimental HEP field that has gone far beyond the situation that was common still in the first half of 20th century when one scientist or a small group of them might produce some interesting results. The "insignificant" right tail in your distribution of papers on number of coauthors contains the hot part of the modern physics with high impact results topped by the discovery of Higgs-boson. And in your next rankings you are going to dishonour those universities that contributed to this discovery."
"the point is that frequent fluctuations of the ranking methodology might damage the credibility of the THE. Certainly, I do not imply here large and well-esteemed universities like Harvard or MIT. I believe their high rankings positions not to be affected by nearly any reasonable changes in the methodology. However, the highest attention to the rankings is attracted from numerous ordinary institutions across the world and their potential applicants and employees. In my opinion, these are the most concerned customers of the THE product. As I already pointed out above, it's very questionable whether participation in large HEP experiments (or genome studies) should be considered "unfair" for those institutions."