It's a case of efficiency. Stalls and urinals take less space than single occupancy bathrooms - which translates into smaller buildings costing less money to build, maintain, heat, a lower impact on climate and also allowing a higher efficiency usage of land.
Besides, most places that have stalls also have at least one large gender neutral single occupancy bathroom with extra features such as a baby station and disability adaptations.
Unless there suddenly becomes a huge demand for gender neutral bathrooms, I don't see why that additional bathroom wouldn't be sufficient to serve people who can't use the regular bathrooms.