As mentioned in the Any% category rules, timing starts on the title screen with "Play" and ends on the congratulations screen. You are free to submit a lax time by starting the timer slightly before the beginning and slightly after the end, or you can time it frame-by-frame if you'd like to be precise.

I personally suggest recording with OBS and timing with LiveSplit. You only need to submit an any% full-game time, but you can track splits too if you'd like.