Percentage of occupancy for the Indoor Water Use Reduction Calculator for the prerequisite- project only has ADA restrooms.

Once again - I have little experience in CI projects, but I hope it will help at least to guide you. 

Per my experience restrooms outside the project boundary are excluded from calculation if project owner can't affect on it (i.e. change smth including fixtures). As I understand - this is your situation, so the reviewer comment is correct (to exclude such restrooms that are outside the project boundary). 
 

Second thing - as I understood your request reviewr left no comments regarding the percentage of the employees that would use the ADA restrooms. Determination of it was left on your discretion. 

So you can go for:

1. "Little head" and assign 5 % of employees as determined for your project (by technical assignment/OPR/ADA requirement or else).
2. Make feasable assumptions, that not only 5 % would use ADA restrooms in the projects boundary, it would be more lazy people and it would be 10-15-20-else percent that would use ADA restrooms, even if they does not require specific features of ADA restrooms, but only due to a reason that it located closer to they work places. Make this assumption clear and falsifiable (in Popper's meaning) and add as an annex to your subbmition documents. 

In my experience open and honest description of your decisions in grey zone (like percentage of ADA restrooms and people with specific demands is not determined by LEED) in 99,9 % would work.

If you are at the stage of dinal review and you are nerveous about it (some contract issues are depends on successful review or other things) - submit a CIR with clear description of your assumptions and calculations. 

Laura, when you say ADA restrooms, do you mean unisex, accessible restrooms that only have a toilet and sink, and no urinals?