Developer: "The in-game timer is based on actual logic (physics) frames of the game. So it would be accurate to how many frames of actual input, AI, collisions, etc happened. It also, as you are probably aware, pauses for things that might run at different speeds for different people, namely loading screens between maps. It also actually slows down for slow-mo effects like when you kill a boss, since the slow-mo effect just slows down how often the logic/physics frames occur but the timer still counts each frame once.

Therefore the in-game timer is the most accurate in terms of comparing speed runs since it counts only actual frames of input, and can't be manipulated by making the game run faster or slower than real time."

https://steamcommunity.com/app/247240/discussions/0/1750142427224743385/