I found this issue in the Bugs forum - it's a property of the turret behavior (AKA "Not a bug") that turret settings are passed to ALL other members of the family even if you change a single instance.
So there is no way to change turret behavior settings on an instance-by-instance basis if the turret behavior is coming from a single behavior in the family. This seems like a less-than-ideal implementation, because it limits what you can do with the turret behavior. I assume there is some under-the-hood reason for doing it this way, but as an end-user I can see no benefit.
So, the only ways to do what I want are to give all turrets with different target lists their own families with their own turret behaviors, OR to add multiple turret behaviors to the common Turret family and only activate the individual turret behaviors needed for each turret faction. So my Turret family would have behaviors TurretRed, TurretGreen, etc. Since it's easier to do one of those than try and write my own turret plugin (which is otherwise working wonderfully, I should add), that's what I'll do. It's messier than I want, but it'll work.
Thanks for your suggestions megatronx, much-appreciated.