There is an option to make the cube flash white every time you reach a checkpoint, but it is hidden in the game files.

To enable it, go to the folder

Windows: C:\Users\<your username>\AppData\Local\Two Tribes\EDGE

Mac:~/Library/com.twotribes.edge/

Open the settings.ini file and change "show_checkpoint_effect" from false to true.

Having this setting enabled can be useful for performing or finding checkpoint skips.