"Timer starts upon gaining control of your character upon the start of the scope the primary target mission and is stopped on losing control of your character after leaving the final.

I found this to be unclear, and know that others were also not sure how the run was timed. There is also a ≈2sec gap between the HUD disappearing and losing control of your character.

My suggestion is to make it so that the timer starts when the objective "Go to [Location]" appears, and ends when the HUD disappears. It is possible to pinpoint the exact frame of when these happen, and in my opinion it doesn't matter when the timer starts/ends, just that it is consistent across all submitted runs.