The only thing that doesn't make sense to me is his rune... why would Melenia have a rune, but not Miquella? Why would Mohg and Morgott both have runes, but only Melenia does? To me, Miquella's great rune is still MIA, unless somehow it was absorbed into Mohg's (which you would think the item description would say). My theory is that Miquella's cocoon is a catalyst to launch the story of a planned DLC, similar to the painting in Anor Londo was in Dark Souls. Saving a Great Rune for the DLC would make sense, since they have a gameplay purpose and not just a story purpose. Also, since you can enter the dream of Godwyn, I don't see why you couldn't enter the dream of Miquella.
Edit: apparently dataminers have found references to Miquella in cut content that support my theory
- Cut content shows that Miquella is St. Trina, god of slumber. "Finally, I have found it..... St. Trina's, no, Lord Miquella's cadaver... Such that I may aid you, O Lord... So please, I hope you welcome your humble servant Rhico... Into your dream, the world of your heart...... Indeed, I beg you grant my wish, that when you transcend from empyrean to god, allow me a place by your side....." - Rhico, cut NPC
- Cut content shows that Miquella's Great Rune is the Rune of Abundance. "Twinblade that contains the power of the Rune of Abundance. The holy power within the blade can call upon part of Miquella's own strength" - Abundance Twinblade
So Miquella is slumbering, and he has a dream. A world, in fact. I am calling it now, we're definitely going to have a DLC set in the world created by the dreams of this sleeping Empyrean. The seeds have been sown. Miquella being St. Trinas also explains why descriptions say there's confusion over whether Trinas was a girl or a boy. Presumably, Miquella could take either form, the same way his "mother" could appear as either Marika of Radigon.