When I did absentee voting, the voter signature and voter id information were on a perforated slip attached to the outside of the envelope.

That way, the process is something like:

1. Look at the slip. Verify voter signature, eligibility to vote, and mark as having voted in the voter rolls.
2. Detach perforated slip from sealed envelope. Sealed envelope now contains no identifying information. (This envelope was mailed inside an outer mailing envelope.)
3. Entire sealed envelope and contents thereof goes into big bin of accepted ballots.
4. Later, election workers open the sealed envelopes from the bin and run the actual ballot papers through the scantron machine.