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Well, it turns out that switching to another Mac (Big Sur, Xcode 13) did the trick. Exported the certificate and copied that to the new Mac with the Packages project file plus the app itself that I could still successfully sign and notarise on the old Mac. Built and signed the pkg using Packages and notarised it with altool.
Very frustrating few days of messing around which I could have avoided if I just switched to the other Mac sooner.