As far as the METAgroup whitepaper Messaging Total Cost of Ownership: Microsoft Exchange 2003 and Lotus Domino in Small and Medium Organizations I have to say it just doesn't look right. It appears to be lacking detail in areas. I would think that the majority of organizations looking to implement either solution would like to be able to compare them in similar environments, such that one could tell what the TCO for one seat in the Exchange environment costs versus one seat in the Domino environment for the same infrastructure. Having all the possible variables available in the environments studied can easily skew such TCO figures in any direction.
I don't recall seeing the number of mailboxes within each industry cited. If given the same number of employees (mailboxes) within each organization, the size of a mailbox in the Professional Services Organizations utilizing Domino would have more storage costs than all eight of the others combined. If you average the size for an individual mailbox across the four Domino environments you are at roughly 262MB per mailbox and the average size for an individual mailbox across the five Exchange environments would come out to about 88MB per mailbox. A quick glance has Domino TCO at about twice that of Exchange, yet in the scenario it would be supporting three times the mail.