You'll want to give the MPR Supplemental Guidance document a close read, especially for MPR's #2 and #3, but nothing in your situation appears to preclude you from registering this as one LEED project. One construction schedule, one CM, one owner.... sounds like one project.
The small size of each building is an especially compelling reason to treat this as a single project, as the soft costs for documentation can become a higher percentage of total project costs as the project size gets smaller. Anything you can do to streamline commissioning, materials tracking, documentation etc. will be worth doing.