Once at the top of the spiraling walkway, sidehop and use the deku leaf to grab the platform behind the Helmaroc King. Align yourself properly, and zombie hover towards Ganondorf's look-out. Hover to the loading zone behind the door and proceed. Note: This trick is necessary if skipping the skull hammer. Otherwise it doesn't save any time.
Skip the first hit in the same way as told for the long hover, by leaf to the ledge behind Helmaroc. After this, take up the rock nearest the spikes on the right side, since this one contains hearts. Make sure you only have one quarter of a heart left. Line up to the spikes and place the rock behind you. Take out a bomb and place it in front of Link, between him and the spikes. Turn around quickly, take up the rock, face the spikes and throw it. If lucky, one or more of the hearts will get on top of the spikes. If so, let the bomb kill you and zombie hover towards it. If you get it, you can jump of the spikes and run up to Ganons door.
Note: The hearts in this trick is totally luck based and might not land on top of the spikes 100% consistent. But, this is the fastest way of skipping the fight by console.
Because of the timing necessary to preform this trick, it is considered TAS-Only. More info to come.
After the third time you have hit Helmaroc King with the Skull Hammer, lure him into the corner near the spikes. After he pecks at you, and gets his beak stuck in the ground, hit him once more with the skull hammer. This will trigger his 'unmasking' cutscene, which automatically warps you to his head. This clips you past the spikes allowing you to skip his second phase.