Steps to have App Control agent(s) ignore CERT_TRUST_IS_PARTIAL_CHAIN errors on the Counter Signature Chain, and rely solely on the Certificate Chain used by the Publisher for the Code Signing Chain.
Publisher[Microsoft (IneligibleForApproval: CounterChainIdx[1] CertId[123] ValidationError[...CERT_TRUST_IS_PARTIAL_CHAIN:CERT_TRUST_IS_NOT_SIGNATURE_VALID:CERT_TRUST_IS_OFFLINE_REVOCATION...