How come certain airports can have unique rotating beacon colors?
The lighting for private heliports is not regulated by the FAA, but by the individual states. The FAA has an Advisory Circular laying out guidelines for heliports, but it is only a recommendation. 


  The  Federal  Aviation  Administration  (FAA)  recommends
  the  specifications
  contained in this AC for all applica
  tions involving development of this natu
  re.  In general, use of this AC 
  is not mandatory.
  
  From FAA AC 150/5345-12F: Specification for Airport and Heliport Beacons


It is only regulatory when the heliport is built using federal funds. In the AC they recommend the white/green/yellow pattern. 

Only a couple of states have adopted the FAA guidelines as regulatory.

The state of Pennsylvania incorporates many of the FAA Advisory Circulars in their state law. For example the ground markings and the lighting for the perimeter of the landing and takeoff area for the heliport are required to adhere to the appropriate FAA AC's. But in regards to the beacon it simply states:


  A rotating beacon is recommended to be installed for night operations at public heliports. 
  
  Pa Code § 471, Appendix A, Criteria I, i)  


It does not even have that recommendation listed for private heliports.

Although it is not in the FAA Advisory Circular some places list the beacon color code for hospital heliports as white/green/red. I can't find anything authoritative on this but examples are at an aviation wiki, on Quora and on airliners.net.

This company that sells heliport beacons indicates that their beacon is "Available in Hospital Heliport version (not FAA certifiable)." It doesn't indicate, but this is likely a white/green/red version. And since it doesn't adhere to the Advisory Circular it isn't FAA certifiable.