Indeed, and the other truth is that over a 6 month season, with injuries, trades, promotions, often the team that finishes in September is quite a different team than the one that accumulated its record. So there is always some lesser or greater degree to which a record doesn't even belong to that current team.
But take it from a different tack: Since in truth we know that the outcome probability of any short series between two baseball teams with between 500 and 600 records is so close to even that neither team should have any expectation of being favored, do you *want* to bias the outcome to the advantage of the team that did better through the regular season exactly as the reward for that performance? That is a philosophical question, not a mathematical one.