It is not the counting of accepted ballots that is the issue, it is the pre-counting handling of the absentee ballots. I presume the signature match goes against the registration data. Signature looks different? What is the registration? “D” Count it. “R” Reject it. Down the line races not voted? Fill in the oval for the “D” candidate. Ballot voted straight “R”? replace it with one of these, shred the original. Lots can be done when the process is unobserved.
In the old South Bronx, a friend worked for the Board of Elections as a young man--this was when it was all Irish. The electorate and the local board were all mobbed-up-union Democrats. But by law, you need both a Democrat and Republican sign-off on everything you do. So every election cycle, a couple of the guys would register Republican for the day, to make sure any action was approved, dirty tricks included.
The ballots we get today are all coded with a number, torn out of a book that retains the matching numbered stub. In an investigation, not just the number, but the tear itself would have to match. So you might have to print duplicates of each ballot book for use if needed. . .