The chain of custody of the ballots is the same as it has always been. You can see the ballot at the scanner, it isn't a hidden process. The ballots are collected and set aside as a paper audit of the recorded ballot. The paper ballot is what is checked by the voter.
Most if not all election security advisors say the paper trail is a must for a secure election. That way the tabulators can be audited with a record of "the intent of the voter" which is what happened in Georgia.
If the ballots are messed with, you would have to know how many of one kind of ballot to pull and for what kind of ballot to replace with. Note that this is not that easy as it would seem for a one race ballot with two contenders because each precinct is also conducting other Federal, State, and Local elections as well. All in all, to pull off a fraud with a paper ballot audit is not going to happen as long as every poll worker in the state in every precinct is not in on the scam.
Well, I think with the paper ballots to compare to the Dominion totals, you could discount (although not completely eliminate,) the idea that the machines themselves changed the count, regardless of the ballots.
However, you’d be assuming a transparent chain of custody. Wood complains that there were several hours where the ballots were unobserved after the polls closed but during the counting process, and that is where paper switching or even adding could have taken place. He has some convincing affidavits to that effect.
I’ve seen a lot of “magic” with technology, so the fact that there are machine-created ballots is enough for me to believe that everyone of those machines should be examined, hardware and software.