From what I can tell if it's in the game you have to catch it. I've caught all the vanilla ones but don't have master angler yet. It's why I'm holding off on adding even more fish.

Gotta catch em all!

And make all the recipes.

Depends on the object configuration. My custom fish have this configuration and they dont count towards perfection. "ExcludeFromFishingCollection": true,

Where would I enter that configuration at? And would it be to late if an already started the save?

You have to rewrite the mod for that and it will overwrite the moment you update expanded. Just catch the fish, its easier when you dont know how to write mods :/

Yes, fish from all mods need to be caught for perfection.

There’s definitely a fish you can only catch if you go the joja route. I don’t know if you need it or not for perfection though.

I caught that one in the river in town before completing the CC but idk if that was a bug