IAQ Concerns due to LEED boundary

My project is inside a 3 story building. The remodel work spans all 3 floors and City permit drawings show work all over the building and building shell. My client wishes to restrict the LEED boundary to the 3rd and 2nd floor (where the restrooms are). We are putting in new stairs going from 1st through 3rd floor. I can establish a cut-off with regards to all other credits, but my concern is for IAQ. How do you enforce IAQ from the 2nd floor up and disregard it below? Would I be jeopardizing all the IAQ credits and GBCI's acceptance of the boundary and ultimately the project? Thankyou in advance...