With the Objective Skips the in-game time is accurate as to when the level ends, however on Mission 9 if the player were to fail it in a run and continue the time would have to be done by hand.

Using in-game time will factor out the time that the cutscene of entering Fortuna's atmosphere wastes, which averaged ~5s over the fastest skip I've ever gotten on it. I think the most I have ever lost to it (once I stopped reseting over it) was around ~10s. It will also cut load times. I've not looked into load times to see how much they very or not nor has anyone else as far as I'm aware. Without the load times runs done on Gamecube and ones done on the Wii would more fair to compare as it stands to reason that the Wii would have faster load times, or at least I know it does for other various games.

It doesn't show the final in-game time in the game itself but it's very easy to calculate, especially if you use something like an excel/google spreadsheet. Just throw in the times and use the sum function and you're done.

Hookshot Skip is NOT a separate category. If you choose to skip getting it that is your choice, but it is still an Any% run and will be put on the Any% leaderboard with everyone else.