The Supreme Court also decided — importantly — that there wasn’t enough time to complete that full recount before the deadline. There were many different ways the election could have been resolved by that court dispute — a recount leading to a Gore victory, a recount leading to a Bush victory, a failure to complete a recount leading to Florida’s electors going unseated, or even a re-vote (which could have led to a Gore or Bush victory).
The court decided the election in Bush’s favor with no further counting or voting. Thus, victory by litigation.
One unofficial recount study completed about a year later suggested that Gore would have won by an incredibly narrow margin if the whole state had been hand-counted by the same standards, but lost if he had gotten the partial recount he wanted or if the standards for counting had varied from county to county.
Bush didn’t win by having more votes. In truth, we don’t actually know for sure, but to the best of our knowledge, Gore probably had more votes in Florida. Not many more; well within the margin of counting error.