The more important is the following. Allessia seems to have been assisted by one Pelinel Whitesdrake, who, by all descriptions I've seen, seems to be an aspect of Lorkhan. According to Polycarp, the Aedra of today are in service of Shor, and not Auri-El (with Akatosh having been fully severed from his Anuic nature). However, when the Divine Crusader was accepting followers, among them was... was he Altmer or Bosmer? At any rate, he joined under the assumption that Auri-El and Akatosh are one and the same.
I take it you are referring to:
"We also know that the present Aedra being worshipped are false gods who came to power in service of Shor." from anolysis on the Aedra. Which seems to be nothing but more of the 'Marakuthi have become the Aedra' hogwash that was in vogue for a while.
Anyway, you shouldn't confuse the Knights of the Nine and the Divine Crusader with Pellinal himself. They were formed after Pellinal was gone and you can't really expect them to share the same views after a good four thousand years.
All this does not fit together. Is Akatosh Auriel, or not?
Ofcourse he is. Though I can't quite find where you are getting the idea from that he's not.
Auri-El (King of the Aldmer): The Elven Akatosh is Auri-El. Auri-El is the soul of Anui-El, who, in turn, is the soul of Anu the Everything. He is the chief of most Aldmeri pantheons. Most Altmeri and Bosmeri claim direct descent from Auri-El. In his only known moment of weakness, he agreed to take his part in the creation of the mortal plane, that act which forever sundered the Elves from the spirit worlds of eternity. To make up for it, Auri-El led the original Aldmer against the armies of Lorkhan in mythic times, vanquishing that tyrant and establishing the first kingdoms of the Altmer, Altmora and Old Ehlnofey. He then ascended to heaven in full observance of his followers so that they might learn the steps needed to escape the mortal plane. - http://www.imperial-library.info/mwbooks/varietiesoffaith.shtml