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Trusted Publisher policies are for authorizing all applications that use the same certificate as the executable (your setup.exe) to run.
If you want to trust the Setup.exe so that all the files it puts in place are authorized to run, you should add setup.exe to a new Trusted Updater policy.
If you want to use the Trusted Publisher policy, then you will need to inspect the certificate that setup.exe is using to identify if it actually is invalid.
Ahhh I see. That clears that up a lot. Thank you.