Given three reference letters in a postdoc application, how to decide which to list as the second letter and which to list as the third?
In my experience I have never encountered a situation in which the ordering of reference letters mattered.
Usually the only distinction between the different letters is when you are required to have letters from your PhD/postdoc supervisor. These letters may carry more weight because they are from the people which can best assess you.

However my experience is from life sciences, not physics.