I agree the lack of site work shouldn't be an obstacle; whether the project meets the MPRs probably boils down to the likelihood of or intent for relocation.
The MPR Supplemental Guidance includes language that states:
"Prefabricated or modular structures and moveable building elements of any variation may be certified once permanently installed and/or established as part of the LEED project building in the location that they are intended to stay for the life of the complete structure."
If the modular structures are scheduled to be relocated, or only expected to remain on site for a limited number of years, then the MPR is probably not being met, but if the DoD is using modular construction but otherwise providing a permanent installation, then the MPR could possibly be seen as being met.
Most GSA projects of this scale require LEED certification, but that policy pre-dated the 2009 versions and may not always anticipate the nuances of particular requirements or situations. You may want to address ambiguity of the MPR language and show how other requirements and pre-reqs are being met, explain how the project may need to submit a CIR to verify the MPR compliance or clarify it's intent for relocation.