When there's no timer in game, or the in game timer is inaccurate/wonky for some reason, then timing is done from the very start of input to the very end of input. So the moment you can start moving starts the timer, and the moment the final boss's meter reaches zero the timer stops.
You must have overlooked it because this is from the FAQ:
How are runs timed? If a game displays a time at the end and this time is tested to be accurate, it will be used. Most game timers don't include times at pause/inventory screens, dialogs, cutscenes etc, so the time can be significantly less than the video length. An example of an inaccurate game timer is one that doesn't save the exact time when a player saves, perhaps only saving whole minutes.
For games without timers, a simple measure of real time is used. When the player first gets control of the game's charcter, timing begins. At the end when control is lost, even if that's after a 'death blow', the timing stops. For segmented runs, timing stops at the first system-dependent activity, usually this is the actual saving. On loads the time either starts at entering a password or when character control is gained. For runs over 3 hours, the seconds are dropped because by that point the slight variations in VCR playback speed can be large.