Cameron,
I fully agree with your analysis but I would add two aspects.

1) Elite Journals: My assumption is that the major costs for so-called elite
journals like Nature and Science are driven by personell costs. That are
professional editors who make desktop decisions because it is too time
consuming to find proper external reviewers for the majority of all submitted
papers; see for example the 38 editors working for Nature Communication: http://www.nature.com/ncomms/about_eds/index.html#close

2) Social Sciences & Humanities (SSH): Professional language
editing is an often very costly part of the review process of SSH publications. That explains high cost per paper in
that fields also for non-commercial venues, see: http://dx.doi.org/10.5281/zenodo.16462