WORLD RECORD RECORDING
As indicated above, this category begins timing upon both map screens being cleared to begin the game at Samus's Gunship upon first landing on Zebes (the file/default location given after escaping Ceres), and this category ends timing the moment the "Super Missile" text box is fully cleared from the screen upon acquiring the pack of Super Missiles which reside within the egg the Chozo statue is holding directly after defeating Spore Spawn.
For better understanding of when timing begins and ends, the Japanese "Super Metroid Hack Wiki" has provided the following visual information.
This category can be completed with (4%) or without (3%) early Super Missiles, which will change how you farm and unlock doors before entering Spore Spawn's room, as well as the Spore Spawn fight itself. The latter is the faster of the two options.
Although having Super Missiles will make unlocking doors on the way to Spore Spawn simpler, and will allow you to use whatever Missile drops you acquire along the way to dispatch the Kihunters guarding Spore Spawn (rather than having to use the beam if a Missile drop does not occur, or spending more time farming), collecting Super Missiles takes around 23 seconds, which is an enormous amount for how short this category is. The only reason collecting Super Missiles would be faster for you is if you, on average, take two rounds less to kill Spore Spawn with Super Missiles than without, because a Spore Spawn round is approximately 13 seconds long.
Although a Missile two-round is possible, it is quite difficult to consistently pull off compared to a Super Missile two-round. You would have to hit Spore Spawn with 3-4 Missiles in the first round and 6-7 Missiles in the second round, compared to striking him with two Super Missiles in one round and a Super Missile with a Missile in the other. The reason why it is possible to strike Spore Spawn up to seven times in the second round is because Spore Spawn will not immediately close his core if struck during the initial opening period of his second round, making it possible to squeeze up to three Missiles in before he has fully opened and is capable of closing his core. Behemoth's run executes a Spore Spawn two-round with only Missiles by landing three Missiles in the first round and seven Missiles in the second round (three Missiles in the opening, followed by four additional Missiles when fully opened).
Excluding Behemoth's, some of the runs currently on the leaderboard were submitted using "start game" timing. The map screens before the file is loaded take approximately two seconds to navigate through, so keep that in mind when looking at times.