Sean, there is some guidance on non-contiguous project boundaries in the MPR Supplemental Guidance doc that you may find helpful.
In a similar situation I received guidance that it wasn't necessary to include the parking in the project boundary for SSc4, although it would be necessary to earn credits like SSc7.
At the same time, the policy with campuses, I believe, is that project boundaries must be set up so that if all the buildings on campus were certified, the whole campus would be in someone's LEED project.