IBC 2902.3.2 location of toilet facilities in occupancies other than malls

I can't speak to that code specifically, however in my experience additions to buildings in the volume you seem to be indicating (i.e. multiple times) are usually manufacturing facilities. As such, I find that their internal operations generally drive the requirements for each addition. I would be surprised if they'd want their employees having to walk through the entire facility just to get to a washroom.

My industrial clients don't always include a bathroom in each new addition, but they rarely would do two additions in a row without adding a bathroom. And if my memory serves me correctly, there is a bathroom within 500 feet of any corner of the plant.

To the question about the entity to approve it, it's the "Authority Having Jurisdiction." The building official in your locality - whether it's a county or a city - will have the ability to approve it. Best bet is for the architect to reach out to the building official or a lead plan reviewer and discuss the local procedure for getting a variance. Also keep in mind that the building official isn't always the final decision. If they give you a decision you don't like, many localities have a review board - the one in my city is made up of appointed professionals, some of them architects and engineers, some of them lay-people in terms of construction and design - that can overturn the building official's code interpretations.