The scenario they exposed as possible is : voter receives a printout paper ballot with the vote selection printed correctly in text, but the included QR code has modified selection(s). That paper is then fed into the reader/scanner/tabulation machine. No further confirmation.
The whole point of the printout is for voters to confirm their selections, the whole QR code step is a design flaw. Just print regular ballots with filled in circles that can go through a standard tabulation machine and still be read/checked by humans if you really need to add a (required) touchscreen interface to the process.
“If an attacker changes only the QR code, voters have no way to detect the change by looking at their ballots, since voters can’t read the QR code. The change might be detected in a manual recount or a risk-limiting audit (RLA) based on a review of the printed text, but that is unlikely given Georgia’s weak audit requirements, which have recently been further diluted.”
It seems very unlikely that lots of votes getting changed would get noticed to me. Maybe I have a misunderstanding of the process. An RLA would help, but Georgia has had difficulty in conducting audits due to incompetence of officials and people not following process rules, QR codes seem like unnecessary complexity.