The principle is quite simple: In Metal Gear Solid cutscenes are rendered in realtime, meaning the game actually loads the level it is currently displaying and you can warp to that location in a playable state using the area reload cheat. For now this option is only possible on the PC version using the F7 cheat key.

Applied use cases:

https://clips.twitch.tv/TastyHeadstrongOkapiRiPepperonis-UAvAiUyBGN7XWQWR

The Idea is to begin he cell as usual, then go to the vent opening to begin the chain of cutscenes with the Darpa Chief. Wait for the third cutscene when Snake talks to the Darpa chief in the cell and area reload. Skip the codec, exit the vent with circle and area reload again to stand in front of the ladder. Equip the level 1 door card and then walk back into the cell from outside to begin the cell fight.

You can teleport from ninja to Rex lair during Otacon's cutscene talking about Metal Gear Rex. Then trigger the lost PAL key cutscene, and you can insert the Normal PAL key. Sadly the journey stops after that since you can not continue forward as the doors require level 6 - but Snake only has the level 3 door card yet.