If we do bring in Majora's Mask, then we have a reason to connect the power the Fierce Deity has to the way Shadow Link could get rid of Ganon's influence. and a reason for the hero to need to go up against Majora at all.

Of course I don't own a copy of the Hyrule Historia, so I could be completely wrong saying what I said above, but it's still something to connect the Masks to the "why, how, and what reason" behind Shadow Link's slight change of heart.