I hadn't considered the fact that Instant Kills have a totally different end screen when setting the timing standards, and it's unfortunately led to a lot of ambiguity and inconsistency. While I think the fairest way to start timing runs in light of this would be to stop the timer at the screen transition after beating Justice and Baiken, the current set of runs didn't mash through the score screen since that was never the standard. Dismissing the score cord animation after the fight is technically the last input, so I've decided to time up to when the score card appears after the fight(s).

If anyone has another opinion on this, I'm more than willing to hear it. But to me, this seems like the most sensible thing.