Feral cats can carry Feline Leukemia which can be transmitted via a water or food bowl so you have to be very careful. I don't mean to cause alarm but I would put a stop to it ASAP and make sure my kitty is tested next time he goes to the vet. It is the equivalent of AIDS in cats and there is no cure. One solution may be to just capture the cat and take it to a humane shelter or clinic. They will usually tame, spay/neuter, give shots, and find a home for him.

Aside from that, cats are very territorial and this new presence is at least very, very confusing to your cat. Get a cat door with a sensor that attaches to the cat's collar and works by proximity if he must go outside. They really aren't that expensive.