I am also not convinced by the inclusion of the R number in the list of examples - it is unlike the others in an important way. The problem with metrics usually arises when the metric is a proxy for the goal. For example, test scores are not the same as knowledge, and so using test scores as a metric can result in teaching to the test, such that the metric is no longer a good proxy for knowledge. But the R number is not a proxy - it is the actual thing we want to change. (Of course, there are many knock-on issues, such as how we measure that number, which do introduce proxies. Discussion of that would be a much more interesting article.)
Which actually points towards the real solution, which is not to simply rely on gut instinct, but to be aware of what you are measuring, and how it relates to what you want to know.