Auto Start: automatically starts the timer when it detects you are loading into the first area. For glitchless runs start your timer at -4.9s to start at first input.

Due to game logic there are two alternating addresses to store the current level. Because of this, half the time the timer will start during the intro cutscene and the other half will start properly when loading into the first level. After the new game text disappears from the screen, press "escape" once to skip the cutscene as fast as possible (1.9s in the false start). We can subtract this from your final time if this is the case.

Load Remover: pauses the timer when entering a load screen, resumes when you're back in game.

Note: I have not tested this with the extended, only the base game