Not shown:
1) Playing through the game normally 10+ times.
2) Carefully inspecting every square inch of it, every surface, nook and cranny
3) consulting with other people who did the same on best ways to bypass every obstacle
4) devising, testing and revising dozens of different strategies
5) Grinding the best routes and skips for hundreds of times.

The highest level speedrunners can put just as many hours as the devs into shaving off milliseconds of a run. Just because they break the game over their knee doesn't mean they don't respect the hell out of it…usually.