floor area for PIf3 vs IEQc8

We received Construction Review comments that the areas reported in PIf3 do not correspond to the areas in IEQc8. We used the definition for gross floor area (see http://www.leeduser.com/glossary) in PIf3, which measures the size of a room from exterior walls. As the middle of a wall can obviously not receive natural daylighting, our calculations for IEQc8 used the area of rooms based on their floor area measured from the internal walls. Has anyone ever come across this issue or received a similar comment? Would you recommend an explanatory note or recalculating IEQc8, so that the floor areas presented are in line with those of PIf3?