When registering a project in LEED Online the gross floor area is used. Gross floor area is calculated from the exterior walls. https://usgbc.org/glossary#gross-floor-area-gfa

When calculating ventilation rates, ASHRAE 62.1 requires that net occupiable floor area is used. Net occupiable is measured from the interior walls. 

What area should be used when determining the number of baseline parking spots?

I assume the number used in the Reduced Parking Footprint calculation should match the gross floor area listed within the Details tab of LEED Online. 

only one 'anticipated type' can be selected in LEED Online when registering the project. i assume the Reduced Parking Footprint calculation can account for the various programmatic space types of the building - which is how the ES Target Finder is created.