There are two issues here both related to the changes to auto save. One of them is relatively minor but could result in lost progress. The other is much more serious as it creates invalid saves that can no longer be loaded.

1: Auto saving is specifically disabled during the Ganon fight. This shouldn't be the case as you can manually pause and save the game at this point, and the file works fine when this is done, with the Master Sword being returned normally if you had lost it. The issue with disabling autosave here is that you could collect an item in Ganon's boss key chest or from a pot in the tower, and then expect the game to save this when soft resetting during the fight, potentially causing lost progress. The previous autosave settings could've prevented this by saving when the item is collected and/or the scene is changed.
2: Although autosave is also disabled during the Chamber of Sages scene after the boss fight, it is allowed at any point of the ending sequence after that. This means that the timed save, which is prevented during the whole Ganon fight and Sages cutscene, will immediately trigger a save when the scene of Ganon falling into the void begins. At this point, the save is now corrupted and cannot be loaded without crashing the game. Autosaving should not work during any part of the ending sequence as you cannot normally save the game at this point.