Now that I read this over again, and I had watched the video, I'm thinking that maybe the OCR is being used to determine which county/town the ballot is for. They of course could do this by hand but why not try to automate it. Plus they've already scanned all the ballots so they have the images, no need to go through all the ballots by hand again.

The guy in the video talked about there being 500+ different ballots in some cases for a state due to needing a different one for each county or town as you have different county/town races. So I guess the thinking goes, if someone took a single ballot and duplicated it say 10,000 times and submitted them, it would be more easily detectable as that town/county's percentage of eligible voters voting would be possibly much higher than 100%.

In this case you could use OCR to read either the names of the people in the races, if that's how they determine which of the 500+ ballots it is, or I'm guessing each of those 500+ ballots has a unique number which the OCR should be able to read.