Does the lease office decide the number of bedrooms for your family's base housing?

Yes based on availability, number of occupants, and ages of occupants.

It's in the army housing regulation, the AR number eludes me ATM but it's there, describing number and type and gender of dependents etc...

Your leasing office would be the POC to start with but Branch, Base and possibly Regional policies may apply and dictate. Generally the size of your family dictates the amount of bedrooms you get but exceptional family members may rate additional space depending on the situation.