They don't cheat - they're just good at the game. Check out the uniplayer runs I linked to in the guide; they'll show you how to get a time under 3 minutes by utilizing the shortcuts and using flow wisely.
I got to about 2.44 or 2.46 from doing that. However, others probably did use the refresh and pause glitch, read through the guide to see how to do those if you'd like, and there's even a video on Serville64's channel showing you how to do the pause glitch.