I don't know why, but I always think of ganondorf as the final boss of the tower, and then the escape and ganon fight are some kind of extra event+battle. Plus, you aren't really in the tower anymore, so yeah.
Is the secret fairy + business scrub shop a separate room, or is it just part of the main chamber? Would you have to enter it for 100%?
Totally agree. Yeah, the secret room should definitely be required IMO.
There is two ways I see it.
1. Do all the trials and end on entering the room with Ganondorf, or landing the final blow on Ganon.
2. If the trials skip is being used, then it should definitley end on the final blow on Ganon.
Any% and 100% should always start and end at the same spot. Any% is still challenging and lasts about 4 minutes 20 seconds. No reason to lengthen it.