No full [[TAS]] of OoT exists yet. However, were one to be created, the traditional practice in TASes is to begin timing the instant the console (emulator in this case) is turned on, and stop timing as soon as the game ceases to be fed input, which would be after the final dialogue is completed.
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The current [http://tasvideos.org/1140S.html 2:33:25] [[TAS]] of OoT begins timing the instant the console (emulator in this case) is turned on and stops timing after the final dialogue is completed. A time of 2 hours 29.8 minutes is given for the final blow on ganon.