Knowing nothing about running Super Metroid, what's the difference in routing between a real time run and a game time run?
Number of doors and time in the pause menu, basically. The game's timer stops when in the door transitions as well as when you're in the pause menu. So if you have a route that takes a slightly bit more time, but goes through less doors the in game timer will be in your favor. Similarly, you can turn off and on things without it affecting the in game time (for instance the varia and gravity right before the baby metroid sucking you) but that time saved won't be enough in a real time run.