From Act 2 onwards, a lot of speedruns seem to utilise a glitch that allows them to ignore all damage to skip puzzles and survive long drops, although I'm unsure of how it's done. How/when is this glitch enabled?

The game enables godmode on the train ride map so that you dont die during the track collapse sequence. Obviously we skip both the train ride and the collapse, so that allows us to keep it for the entire run