I think it would be cool if there was a speedrun where you try to get as little checkpoints as possible.
Of course once a new checkpoint skip has been found every run that grabs that checkpoint is automatically disqualified.
Maybe there could also be a low% for Vex 3?
I don't think that every run that grabs a newly skipped checkpoint should be disqualified. I know the category is called "low%" but imagine 5 runs on the leaderboard that grab, let's say, 15 checkpoints. If a new checkpoint skip were to be found, and only 1 player does that skip, there would only be 1 run on the leaderboards. Even if the run is 20 minutes long, it would still be first place. So, I think it would be better to just add time to other players' runs if they grabbed a newly skipped checkpoint. The added time would just be the amount of time it takes to skip the checkpoint.
Basically, what I'm trying to say is that mods should add time to the run if it grabs a recently skipped checkpoint. They shouldn't remove it from the leaderboards entirely.