At first blush I like that idea.
It's traceable and verifiable.
The anonymity of the vote needs to be preserved. A ballot traceable back to an individual voter is a non-starter.
However, all blank ballots need to be treated like printed money, with the same security and accountability for every single ballot in every single step of its journey from the printer, to the voting supervisor, to the precinct, and back to the voting supervisor must be maintained as if they were $100 bills.
Start at the printer, and all blank ballots must be serialized and accounted for. Overages or spoiled printed ballots must be accounted for. Ballots must be kept secure and all ballots must be accounted for at all times.
During the election, the specific ballot serial number ranges delivered to each precinct must be recorded electronically. Every ballot serial number issued to a voter must be registered electronically with a time stamp. Any ballots issued to a voter after the polls close is grounds for an immediate criminal investigation. At the time of issuance to a voter, a stub containing the serial number is removed from the ballot, but the stub is retained for later audit.
After the polls close, all unused blank ballots and issued ballot serial number stubs must be returned to the voting supervisor, and must be made available for later audit. Any discrepancy between the number of ballots issued to a precinct and the number of unused ballots and issued ballot stubs returned must be investigated, criminally if necessary.
Post election, any candidate has the right to request a full audit of unused ballots and issued ballot stubs, cross referenced to the electronic ballot issuance files with time stamps. Reasonable costs of such an audit to be born by the candidate, unless evidence of significant discrepancies is uncovered during the audit.
That would greatly reduce the ability to stuff ballot boxes after the polls close.