These were limitations that existed in the equipment in the time. (The uncountable ballot rate in newer optical scanners is vastly lower.) It only became a “concern” because of Gore’s hand recount strategy. (And burning a ton of time pursing the selective recount, which the Florida Supreme Court put a stop to.)

The fact is that with a 1-2% error rate, you can’t reliably “measure” an election result that’s within a tenth of a percent. The whole attempt to recount spoiled ballots was gamesmanship on Gore’s part. (Permissible under Florida law, which was written by idiots, but gamesmanship nonetheless.)