Thank you for the thorough breakdown of when and how the error message triggers! It’s a huge help in troubleshooting!
The missing element is a normal part of Papyrus Author that’s added during installation. Having it missing would suggest, that a security feature of your computer has removed it.
The security feature can be either the macOS App Translocation, or if your mac has an antivirus, it may have quarantined it.
You can check your antivirus’ quarantine files, and see if it has locked up parts of Papyrus Author.
For a quick fix, you can install another copy of Papyrus Author on your computer, and use it. Your work is ready to use, and the second copy of Papyrus Author already has all your preferences applied.