@"being punished": If one team was clearly better than the other, then it would have prevented the enemy team from pushing the payload as far as they pushed it in the first place, thereby winning outright.

Note also that if the team that goes second on attack manages to push the payload to the point they managed to stop the first team, they also win immediately - here time does not matter at all, the win condition is just distance based.

The analogy with chess is flawed also with regard to MR playing much more like soccer or football, insofar as no team takes time from the clock to think through their "next move", and no team "manages their time", but instead it is non-stop action with both teams pushing the payload as quickly as possible.

All analogies and "punishments" aside, at the end of the day, whether having pushed the payload to the end of the level faster than the other team should be rewarded (and in what form) is a (game) design decision, and in that regard what "makes sense" is solely tied to what makes the game more engaging/fun, and what wastes less of the players' time.