The person you replied to is talking about ballots that are just on paper, filled in with a pen, and scanned. So there's no computer making printouts.
Only if the scantron shows that each position on the ballot was counted and the voter is not allowed to leave until the person monitoring the scan confirms with the voter their ballot was scanned would this give confidence. Any issues with the scan, and the voter is allowed to correct the issue. There should never be an issue of reading the ballot by the scanner as an acceptable outcome.
of course, all of this is assuming in person voting only
It might slow things down a little bit, but making sure that the machine can detect a vote for each race/question (even if it's just "Abstain") would make sure people didn't forget to fill out something and help prevent the fill-in-the-bubble equivalent of hanging chads.