You are exactly right. And furthermore: the judgment in Bush v. Gore dealt with the procedure for electing the electors, which is manifestly a federal matter. This matter is handed over to the several states to manage as each sees fit according to custom and technology, but the Supremes, rightly by 7-2 vote, determined that the Florida Rules were not proper.
Now, to exend that logic would mean that ALL Presidential Ballots must be consistent throughout the nation, but the Supremes in Dec. 2000 made it clear that their decision concerned only the current set of facts before them.