I have hitherto just sort of assumed that an animal companion generally tries to stay near its master unless given commands or presented with strange situations. I may be wrong about this premise, but if not then it seems the "come" command is entirely superfluous outside of some very specific situations in which the rules as written are interpreted in a very pedantic way.
If we assume the animal companion is generally traveling with its master, then the "come" trick only becomes necessary when the animal otherwise would not come toward her. Such situations can only arise when the animal is not already with its master, such as when it is fighting — via the "attack" trick or otherwise — or has been instructed to do something else such as "flee," "perform," "seek," or "stay". In the specific case of fighting, there is a specific command — "down" — which explicitly exists for the purpose of disengaging combat. If we suppose that "down" must be used to effect a disengage; i.e., that "come" or "heel" would be ignored in such a situation, then we may also assume the animal will adopt whatever its natural behaviour is after it backs down.
If my initial assumption above — that barring exceptional circumstances or explicit commands an animal companion will generally try to stay near its master — is correct, then the result of "down" seems to be the same as "come". If my second assumption — that "down" is explicitly necessary to effect disengagement because "come" and "heel" would be ignored in combat — is true, then "down" effectively replaces "come". If my initial assumption is not true, then "come" is necessary once the animal companion has disengaged, because the animal companion does not automatically return once it has ceased fighting. But must an animal first "come" in order to "heel"? If so, then there must exist some minimum distance between animal companion and master beyond which "heel" does not work. If such a minimum distance does not exist, then "come" is unnecessary and "heel" does the job just as well. And if an animal companion would accept the "come" or "heel" commands in combat, then "down" is also superfluous.
If these arguments seem absurd or contrived to you, know they also appear so to me. I am wracking my brain for a reason why anyone would use a trick slot for the "come" command when it seems to me as though "heel" should work in every situation "come" would work, and has extra functionality.