ASHRAE 62.1-2007 is mostly concerned with ensuring the interior spaces are receiving enough outside air under the worst-case normal operating conditions. Worst-case conditions are described as those when the least amount of outside air is being delivered (e.g. dampers squeezed down to their minimum openings). If these supplemental units installed by the tenants are never off, then it would be wise to test them -- it would help show that the minimum requirement of outside air is indeed being met for those spaces.
However, if the supplemental units are not constantly on -- for example, if the unit is an AC window box that is only used in the heat of the afternoon -- then you do not need to test the supply CFM. Worst-case conditions in this case would be a cold day when the tenant decides not to use the AC. It is on days such as these that ASHRAE wants to make sure the interior spaces are getting enough outside airflow.