Well, the answer is in your post. Pets are allowed on intercity trains. You use common sense and a pet is a small domestic animal (Dogs, Cats, Rabbits, Llama's) but not Horses, Giraffe's Lions, Whales and Sharks.
Ones that behave (like Dogs) go with you some in a cage with you (like a Guide Cat or Rabbit) ones that don't (like a Zombie or a Werewolf) are more suited to the Guards Van.
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