The signature match is done by comparing the signature on the ballot ENVELOPE against the signature on the voter registration record. The ballot itself does NOT have a signature, so as to maintain privacy.
Once a ballot is removed from the envelope, it then gets mixed in with all other ballots and is counted. If you count those ballots again in an audit, you will (or should) get the same totals. It is not possible to exclude the ballots that did not have a legal signature match performed once they’re mixed in with the other ballots.
How can a mail-in ballot not have a crease? We saw that n0n-creased ballot flying thru the machine.