I saw a deposit run that stayed on 00:00 while it had already started and he was moving, and it allowed him to get where you put the breaching charge in 1 second. While on my runs it doesn't do that and I get there at 00:05.

Isn't this a bit unfair and why does it happen?

I could be wrong, but from what I know, the start of the timer doesn't need to be super accurate. You can start/finish it slightly off from the true time, and any misalignment is accounted for in the actual run time when the run is verified.

The only way I can think of where this would be untrue is if the final run time on the website is equal to the in-game timer at the end of the mission, regardless of the time offset. If that is the case, it could either be a situation where they're taking advantage of a rule that allows them to take that extra time off, or it could be a situation where the mods just made a timing mistake, which with a game this popular for speedruns, wouldn't be unlikely.

I'm almost certain that: • The character can move while the game is loading • The timer at the end is consistent

Oh okay if the timer at the end is correct then all good. Thanks!

I should remind you still that some full game runs need a timer, just in case that's what you're going for. (Read the submission rules)