There's a couple reasons I can think of. You could drop it to go out of your way to get a collectable, then die for a faster send back than having to actually go back.
You could drop it to try out a difficult segment you don't have much confidence on.
You also can stand on top of the checkpoint for extra height, so that's another reason.
I do agree the mechanic could have some more juice squeezed out of it though. I particularly like the idea of throwing the checkpoint to a place you couldn't reach yourself, for example....