Yeah this stuff is crazy, there is so much you have to do to get that time. aside from crazy timing and positioning of bombs and shots. Like:
Arm pumping, when you L-R constantly, it moves Samus ahead one pixel so you can run faster.
Sub-pixel-positioning getting items and getting stuck in doors.
and Thus x-ray climbing technique to get into Tourian, climbing something like 11-14 screens and jumping in near the middle of the screen.
Mockball, to get faster rolling speeds, you run at top speed jump, push down while in the air to look down, press down when you hit the ground and forward to roll.
Spike jumping, where you flip into something that will hurt you, before hitting you return the d-pad to a neutral position then during the getting hurt animation you hold the opposite direction to flip back really far.
there is so much **** you can do in that game. That save thing he did, it has something to do with the game data, where it saves the rooms you can go to through other rooms, saved in a variable, the room that he dies in has changed that value to what a value he needs to be able to skip that part.
If you want to read more on it,
http://forum.metroid2002.com/index.php/topic,6016.msg166883.html#msg166883 is the original person who found this method out I think, I am not sure if he did this one too, but at the least he inspired it I think.
www.metroid2002.com for crazy other techniques.