Hi all, Oxy949 here!
In the upcoming update (probably 1.5) will be changed a highscore system. For now checkpoints don't amends final score. After 1.5 update every restart from checkpoints in the solo mode will give player -1 000 points penalty and reset current combo.
This changes made to prevent players from infinite replaying, aimed to get the maximum possible score.
As a result of the update, leaderboards will be wiped. (Actually, there is a plan to wipe the leaderboards every month or week, but it's not implemented yet)