Personally I believe that no rule changes should be made after the draft, under any circumstances, including extending the season. If you did want to change the rules, then I think it should have been done only if everyone in the league agreed.
And you said it yourself; the extra game is not a regular season game. It's a one-game playoff. Since it is a playoff game, it should not be counted as a regular season game.
Ball Breaker Keeper League: Beast Mode 8-5 #2 seed