I think RTA still remains effective, most runs are done by RTA timing, in-game timing can be inaccurate at times, some games are accurate with in-game timing, but many times are off, or if you die it resets the timer, or still adds time and it can be weird, or off.
Unless we ban loading safety saves, or ban dying (lol) then that presents perhaps the biggest problem.
Often, in-game timer is simply based on frame count, and can slow down and speed up depending on what you're doing or if you're loading, etc. And if the in-game timer is even 0.1% off, that adds up over the course of three hours.
Plus, the timer does seem to continue during load screens from some preliminary testing.
So I also think we should continue using RTA.
If we wanted to take a step toward balancing PC system to system, then an autosplitter that pauses during load times could be interesting... but at this point it's not feasible unless one of you knows someone who will do it.