Firstly, maintaining a feral colony helps to prevent new cats from wandering in and taking over. A properly maintained colony with population control will establish territoriality and other strays will, by nature, not move in. Since this established colony is properly vaccinated by FoF and all animals are fixed this colony can help prevent the spread of rabid animals into an area. Remember also that all of these colonies that FoF maintains are supplied with food on a regular basis to prevent the cats from wandering. Without this managed colony feral strays would move through killing songbirds, attacking domestic pets and tearing open trash looking for food, all the while bringing diseases with them that the FoF cats are vaccinated against.
As for the ear clipping, it is a sign to animal control that the animal in question is spay/neutered and vaccinated and is part of a managed feral colony. If I remember correctly, Animal Control has a policy that it will not pick up feral cats that have a clipped ear because they are fixed and vaccinated.
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