They are using paper ballots. The problem identified here comes from the counting process, and hand counting with similar audit records could end up having the exact same problem if the count audit ledgers were shuffled by similar means. The ballots are shuffled in the audit logs because it is known that a time/order correlation problem exists (ballots tend to be counted in the order they are cast), but the reason that Dominion uses a poor method of randomization, and that some (but not all!) election administrators include count sequence numbers in their publicly released records at all, seem to come down to a lack of care.