So, it turns out that the rules state that the timing is from gain of control, to last hit on the boss, a couple things about this:

Murphagator has used SDA rules to time his run, that gave him a 14:13.

If we use the timing method that's on the rules, his time would be a 14:12.786, according to what I could retime with avidemux on his youtube video.

I've also noticed that if you fall on the pit, that makes the game "end" faster, or lose control of the character faster. Was the "last hit on final boss" made to "shortcut" this?

I guess I don't recall if the 'last hit' was in the rules when I became a mod, but I'm guessing it was.Based on your last statement a way to shortcut either character control or the end screen transition tells me that last hit is probably the most appropriate thing. The concern would be if there was a way to deal the final blow and then die, thus managing not to finish the game after all. I'm assuming this can't be done, but I don't think I've checked, maybe you tried it?

As for the timing, I'm pretty sure I re-timed Murphagator's run along with the other top runs when a number of us came on board. Since there wasn't a need for ms I timed to seconds and I hate the convention of rounding down. To me if your run is really 14:12.786 a claim of '14:12' is misleading. There is definitely a period of 14:12 where you have already started and have not yet finished.

I guess if we find that you can fail after the final hit maybe it makes sense to change to screen transition, though I suppose it won't affect the times much.

This doesn't have anything to do with the timing, but I guess the thing I was thinking about the other day was the enemy AI. If you could figure out a way to keep them from ducking that would probably save quite a bit of time. May be worth doing some research.

Rounding up doesn't make justice to the speedrun, imho, maybe it would be a good idea to add ms to the run at least if it's the WR, but that's up to you guys, just a small opinion.

About dying in the last boss, I've tried it, there is no way to die after beating the boss, the game just "ends" faster.

In fact, murph says that's the way to end the game in his speedrun. I'll test it a lot next time I stream and make a highlight out of it.

I guess we can agree to disagree on rounding.

As for the ending there is a better way to try it out than just testing a lot. I checked it out with the TAS tools and the results are interesting. If you are on the last pixel and deliver the last blow by hitting B and down on the same frame the game will blue screen and hard lock right after the TV host appears. Press down any later and the end cutscene plays as normal. The fade to black happens on the same frame whether you suicide or not. I'm guessing suicide being the way to go was just for fun not to save time. I think all of this supports last hit as the place to end the timer. Even if you are foolish enough to double KO, the cutscene does start, so I'd say that counts as completing the game.