Now, back to the excellent question about scoring. Glad you asked. There's a lot to unpack here and we'll go bit by bit:
-- A ball that bounces over the wall is not an automatic ground-rule double any more than a ball that goes over the wall is an automatic home run in that situation. Remember Robin Ventura hit a ball over the wall for what should have been a walk-off grand slam. Alas, his teammates mobbed him at second, so he never got to home and, thus, never got a home run, never got a grand slam.
-- The players actually do have to run out the homer for it to be a walk-off homer.
-- OK, so here we are at the weekend and the ground-rule double that wasn't. Part of the decision here is that Harrison Bader did not run out the rest of the play, so it could not have been a double. And that's part of the conversation. The bigger part, the rule book says the game ends as soon as the go-ahead run scores -- and if the hitter has to go 180 feet to get the player home, then it's a double, if he has to go 90, then it's single wherever the ball goes.
-- The rule for this is 10.06 (f) and 10.06 (g) in the rules of official scoring:
"Subject to the provisions of Rule 10.06(g), when a batter ends a game with a safe hit that drives in as many runs as are necessary to put his team in the lead, the official scorer shall credit such batter with only as many bases on his hit as are advanced by the runner who scores the winning run, and then only if the batter runs out his hit for as many bases as are advanced by the runner who scores the winning run.
Rule 10.06(f) Comment: The official scorer shall apply this rule even when the batter is theoretically entitled to more bases because of being awarded an “automatic” extra-base hit under various provisions of Rules 6.09 and 7.05. The official scorer shall credit the batter with a base touched in the natural course of play, even if the winning run has scored moments before on the same play. For example, the score is tied in the bottom of the ninth inning with a runner on second base and the batter hits a ball to the outfield that falls for a base hit. The runner scores after the batter has touched first base and continued on to second base but shortly before the batter-runner reaches second base. If the batter-runner reaches second base, the official scorer shall credit the batter with a two-base hit.
(g) When the batter ends a game with a home run hit out of the playing field, the batter and any runners on base are entitled to score."
-- So you see how the Bader turnback and the rules regarding the end of the game and awarding of bases here works in concert for the final score and the walk-off "ground-rule" single.
Hope that helps.