The fact that the Dominion machines completed and printed the voter ballot from an electronic touchscreen is a big red flag for me. So they print the ballot, it gets fed into the machine (but it’s counted by a non-user readable code - this is true), then what happens out the other end? What’s the chain of custody once that ballot is inserted into the counting machine and comes out the other end of it and ultimately into the hands of the hand counters?
Exactly.
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.