It isn't really explained what Fierce Deity is, or why he was turned into a mask. I have tons and tons of ideas about what he could be or how or why he was turned into/put into a mask, and Hylia sealing him felt the most plausible of all of them. We know that he's tremendously powerful, possibly so powerful that only Hylia herself could seal him away. Perhaps, though, there was some relationship between them before he had to be sealed away - as Hylia and Demise were the original Zelda and Ganon, perhaps Deity was the original Link. Purely speculation on my part though!