It seems reasonable to exclude the garage from the project boundary and still use its spaces for SSc4.3 and 4.4. Version 2.2 was less prescriptive in stating how the site boundary was to be defined, but we've seen car share spots such as zip car used for 4.3 and 4.4 that were outside the LEED site boundary.

One thing to check, though - if there are any parking spaces that are closer to the building than the ones in the garage, those would probably have to be the "preffered parking" spaces for SSc4.3 and 4.4.