Well . . . . the desktop is running Linux so portable Calibre isn't an option AFAIK (and the drive is an internal 3.5").
It sounds like the sequence I proposed will technically work (and I need to include metadata.db in any rsync process), but I need to be
VERY careful about the sync. In particular, I need to ensure that there are no changes on the desktop while I'm on a road trip or I'm going to be doing manual updates for every book that changed

In the end, I'm letting rsync answer my original question about how to diff the libraries - doing it at the file level.