I have not played parkour yet but from what you say I think it is for a challenge, if you go through the optimal route it is at your own risk because if you fall then you return to the beginning, but if you do not fall, you will most likely win without any checkpoint, you have to be smart when choosing the routes.
The problem faced is that even if you skip a checkpoint and hit one later in the level, it doesn't count. Why should you be so harshly punished and sent back to the beggining when you work so hard to get far ahead of someone, the better parkour player should be rewarded for the win, not the person who takes the time to try and hit all checkpoints without missing one.
Checkpoint pressure plates are sometimes very inconsistant aswell so running over one may not actually count sometimes due to ping and lag which you should not get punished for either.
Your point here i feel is extremely flawed and I highly suggest playing parkour so you can understand why this suggestion is being made. It is quite a fun gamemode and this change should encourage more players to play the game.
The amount of times players leave because they fail a jump and are sent back to the beggining is quite alarming and those players probably stop playing the game because of it. So surely cubecraft would want to discourage this and create a more user friendly game right?