This is an ambiguous situation and I would recommend you check with GBCI, since USGBC has not not issued official guidance on multiple buildings in this kind of situation.
I would see these more as horizontally attached buildings than as vertically attached buildings, since you are looking at two separate towers connected at the base by shared infrastructure.
I recommend reading LEED's Minimum Program Requirements for some indications on how USGBC might handle this. Since HVAC and functionality of the buildings are separate, I think there is a good chance they can be separately certified, but it's hard to say. Could the garage be considered a "public utility'? If so, that would help your case, per the guidelines for vertically attached buildings.