Currently if a pack dev were to include the blacklist in a pack it'd overwrite the user's data every update. I'd like to suggest having the blacklist in a separate file

Can it maybe grab the blacklist from JEI?

index customization can be done via resource pack. please see the wiki for more information.

Kat is correct, the local edit mode hidden stacks are per user, but can be copied to a resource pack file shipped with modpacks using common data scripters/loaders like KubeJS. That is to say this suggestion already exists.