I know as of right now, the leaderboard is being judged by real time rather than the in-game timer. I wonder if there's any exact reason for this? It's just a bit odd considering that the in-game doesn't count loading screens and seems more fairer for people who have to endure longer loading times than others. But there's still some use for the real timer considering for example "The End" level doesn't count in-game time even though it's on, that time just stops after completing the Air Base level; a real timer could be used to manually count what time it completes that level.

Runs could be judged by the in-game timer but they still have to be submitted with a real timer in order to calculate the remaining in-game time for "The End" level and then added to the final in-game time that the player finished the Air Base with. Just some food for thought.