That isn't an issue. The sites are the transmitters that carry the radio signal. Departments, in the case of trunked systems, have the talkgroups for the agencies that serve a jurisdiction.
When set up as they should be, here is what happens: When the scanner is located in the "footprint" of the Department's location circle/rectangle, the scanner will "open up/unmute/unavoid" the talkgroups and allow radio traffic to be heard. When outside of the Department foorprint, the scanner should more or less, Avoid/Lockout those talkgroups associated with the Department.
So in the case of sites, their location ought to be a circle because generally, radio waves radiate in a circular pattern. How far out those radio wave go is a function of the "horsepower" of the transmitter. Simulcast systems use a network of several transmitters all using the same frequency to ensure signal saturation of the area, particularly in-building construction. Now these multiple transmitters can be arranged/sited/located so that a rectangular coverage is achieved. But it is like placing a series of overlapping circles.
Departments, as mentioned, are collections of talkgroups assigned to a jurisdiction. The database uses the center point of the jurisdiction for the location (subject to modification by the scanner user). The database, for better or worse, assigns a circular area (again subject to user programming).
So you can have numerous Departments all having different areas, still using the same site. Kind of like several boxes under a big umbrella.