Am I correct that Supercast notifications are separate from Warpcast (and any other client)? Meaning, clearing notifs on Supercast will leave them unread on Warpcast?

Is this always going to be the case?

(mostly curious / academic)

Yes, you are correct. Supercast notifications are separate from Warpcast and other clients. Clearing notifications on Supercast will not affect unread notifications on Warpcast. It is likely to always be the case, as each client likely maintains its own notification system.