Honestly, exactly when the reactor timers split is not important for speedrunning. The main problem with the current system is that there is unrecorded game time. I could have a 30 seconds speedrun with an hours gameplay in it.
If anyone has ever done any speed running before or follow speedrunning in general you are probably aware that, almost universally, time begins when start is pressed and ends when the player loses control of the game (or a agreed upon easily marked point.) At no point during the run can the timer stop. The exception to this is that some games are timed using their In Game Timers (IGT) which are not active during loading screens and menus. However, there is never any gameplay that is not timed using this method, or its not used.
Its not a huge problem. A game with unusable IGT is just timed using Real Time Attack (RTA). The only downside there is that it requires an external timer (no big deal), and the actual speedrunners aren't using the function that was supposedly made for them.