You are 100% spot on. The problem is that they have convoluted the counting and verification processes. I can tell you a precinct can easily process hundreds of thousands of ballots before the end of the day. As long as the ballots are identical, the counting machines are calibrated, validated, re-validated, then certified, it can be a continuous process throughout the day that culminates in a finished count within an hour of closing.

1. Stack ballots in groups of 100 … just like cash bills are.
2. Run them through the counting machine. Take that stack to a separate staging area that again runs the ballots through a counting machine that just counts the number of actual ballots. Again, line a bill counter.
3. Bundle in stacks of 100. Move those to a validation room,
4. redo the entire counting process from votes to ballots again.
5. If there is not a 100% match to the first count, isolate the batch, send it to the ‘curing team’. Find the issue, remove bad ballots, return good ballots to the front if the que, go again. Votes ARE NOT added to the reported totals until the stack is counted, recounted, then validated. SUPER EASY.

100 ballots shouldn't take more than 5 minutes to run through the entire process. It is a continuous process so you constantly have several batches processing at the same time.

If Chik Fil A can pull off what they do, Im pretty sure we can come up with a dummy proof, super secure and easily verifiable process.

EDIT: if a race on a ballot is not voted on by a voter, it is still counted as a ‘Null’ vote. You do that for accounting purposes. All races should have exact same number of ‘votes’, including NULL votes.