Kristen,
It's important to keep in mind that LEED uses ASHRAE as a reference work, but can and does modify certain sections to only apply to itself. In this case, you're absolutely correct in how ASHRAE is worded, however, you only must comply with the parts of the standard that are within your scope. Therefore, you should have automatic shut off controls on all lights within your buildout. The rest of the building is outside of your scope and therefore does not need to comply with 90.1-2007.
Paul