I think it's possible that from an engine balance and longevity standpoint, maybe the motor is happier with the mass in it.
But I don't see how the wheels know where all that twisting force is coming from. You could have two flywheels with the same exact rotational inertia....one from a dense material like iron that's small in diameter and long, versus an aluminum one that's bigger around and narrow.
It all just comes out to foot-lbs of energy storage, methinks. Work to accelerate = work to decelerate. You store up the energy on the line spooling it up, and you get it back at the end of the track when the sled goes *wham*.