Zones served by mutli-zone unit but is exhausted separately

Regularly and non-regularly occupied rooms must be provided with outdoor air.  Unoccupied rooms are not required to be provided with outdoor air.  If the rooms served by the multizone unit are regularly and/or non-regularly occupied, then they will need to be included within the vent calcs.  

Yes, regularly occupied spaces must be included within the ventilation calculator. 

  I think I have a better understanding of your project specifics, and now understand why you are questioning that regularly occupied rooms should be entered into the ventilation calculator if all outdoor air that is provided will be exhausted rather than returned to the air handling unit. If the room type more closely aligns with a room type listed in 'Table 6-4 Minimum Exhaust Rates' of ASHRAE 62.1 then you do not need to include it within the ventilation calculator - even if it is considered to be regularly occupied.  For such scenarios we provide the following narrative with our LEED application: "Project includes rooms that are regularly occupied however they have been excluded from the ventilation calculator. The ventilation of such room adheres to the exhaust requirements listed in Table 6-4 of ASHRAE 62.1" HOWEVER....."Art Classroom" and "woodwork/metal shop" space types are listed in both the ventilation table: Table 6-1 and the exhaust table : Table 6-4. My opinion would be to include them in the ventilation calculator since 'art classroom' and 'wood//metal shop' are selections. Since they are being exhausted per Table 6-4, they should not create problems within the ventilation calculator...in other words, I would not expect that you would need to provide more outdoor air when compared to the exhaust rate listed in Table 6-4.  Hope this provides better direction. Great Question!!