As Paarthurnax said, Alduin was "Akatosh's Firstborn" and Alduin as well says that he is an "Aspect of Akatosh". (I say Akatosh and I imagine the game says Akatosh not because they mean the Cyrodiilic entity but the Et'Ada Alduin/Auri-El rather than the dragon Alduin) I take this to mean several things. Do recall that the Aedra as a whole cannot directly act on the Mundus as Daedra can, and when they do, it's typically through some vessel (A Shezarrine, the blessings of priests and shrines) or avatar (Wulf and the other avatars of the Nine in Morrowind are fine examples). So what if Alduin was enforcing Akatosh's will as an aspect of him? The ability to bring dragons back from the dead not via necromancy but as if they had never died thing is not only defying Arkay's sphere, it goes and defies Akatosh's own sphere by essentially rolling back the cycle of time for a set being.
As for the Dragonborn? That could be Akatosh's other schizophrenic half, another Shezarrine (which I prefer, as Lorkhan is referred to in some stories as a dragon as well, and in most religions, Akatosh has replaced Lorkhan and even now Talos as the guardian of Men), or what-have-you. Mythic forces of belief-is-power, and mass belief of Akatosh's current role in the pantheon, could indeed reshape the actions of gods to oppose themselves. Note that there are still a few people that follow the Old Gods of Skyrim, but they are few in number and religion is largely Imperialized by 4E201