This process is absurd to me.
Where I voted in rural fly-over hillbillieland (Pettis County, Missouri - which has its own political shenanigans to be sure) we deposited our ballots directly into the machine to tabulate them at the polling center. The machine sat atop what appeared to be a secure bin which held the ballots, presumably resistant to tamper.
Before I was handed a ballot, my license was scanned and voter information verified against the county record (little old ladies operating tablets with scanner attachments, clearly backward hickville). Then I was handed a ballot corresponding to my exact district with my electorate and issues. Last month, I received a sample ballot of different physical dimensions and card stock from the ballot used, containing every issue in its exact wording (as well as every candidate as they appeared on the ballot).
There was never a time where I was separate from the ballot before it was submitted into the machine. The results are uploaded immediately after the polling center closes and the county election results are known within minutes of the election concluding.
I suppose there could be the case where the poll workers just filled out extra ballots and crammed them into the machine, but I can only imagine that when my ID was scanned, a process added my presence to a total in some section of memory and if more ballots are cast than people who show up - that would be cause to draw the results into question.
This whole nonsense of shipping ballots around by milk crate is way too advanced for me to understand the benefits of it, apparently. Absolute space age levels of enlightenment and sophistication.