A friend of mine (owner of a donut shop) had a similar problem.
He needed the bathrooms to be handicap accessible. That does not mean an extra stall it just means that the existing stall needs to be wider. Since he owned 4 shops total and one was small, in the small one he combined the men’s and women’s rooms into one and put a passage lock on it. That seemed to satisfy the town.
The plumbing code requires separate restrooms for men and women in restaurant/food service occupancies. I know owners often switch to one restroom being private for employees and the other for the public but that is done after the C/O is issued.