If there is one consistent thing about the building code is that it is not always consistent. Sometimes the code makes reference to specific sections and sometimes it doesn't. For example, in Sections 420.2 and 420.3, it stipulates that dwelling units must be separated using fire partitions and horizontal assemblies in accordance with Sections 708 and 711, respectively. However, Section 420.4 states that smoke barriers shall be provided in Group I-1, Condition 2; but nowhere does it reference Section 709. Does that mean a smoke barrier in this application does need to comply with Section 709? Of course not. The same situation applies between Sections 2902.2.1 and 1109.2.1
Section 1109.2.1 is the parent paragraph for all family or assisted-use toilet and bathing rooms. It basically establishes where they are required and all the following subparagraphs describe how they are to be designed. Just because Section 1109.2.1 mentions assembly and mercantile occupancies, does not mean that family or assisted-use toilet rooms used for other applications or as permitted by other sections of the code need not apply to the subsequent requirements for those types of toilet rooms.
As for the meaning of "use," it seems the meaning is more in line with what you said, but the exception would still be permitted in this situation. Here is what the
Commentary states:
Exception 3 specifies where toilet rooms are clustered
together (i.e., entrance doors next to each other
or across the hall), not all need to be accessible. In
such configurations, typically found in a doctor’s
office or drug test center, the requirement is reduced
to a 50-percent minimum. If these toilet rooms are
clustered in separate locations, such as in a multiclinic
facility, the 50-percent minimum would be
applied to each cluster. A single-occupant women’s
bathroom adjacent to a single-occupant men’s bathroom
is not considered a cluster since they each
serve a different sex. The IPC does have an allowance
that would let some small occupancies have two
unisex single-occupant toilet rooms, rather than having
the same rooms labeled men’s and women’s (see
Section 2902.2.1) If these toilet rooms are clustered,
they can use this 50-percent exception since they are
the same type.
In the OP's situation, each toilet room can be a family or assisted-use toilet room per Section 2902.2.1. Thus, it is one type of "use"; therefore, only 50% (or one in this case) needs to be fully accessible.