Near the end of her reign, as Alessia lay dying, she was visited by Lorkhan, called Shezarr in Cyrodiil. He brought with him a pact from Akatosh, the chief of all gods, for Alessia. Akatosh infused Alessia with his own divine blood, then had Shezarr place her soul into the newly formed Amulet of Kings. Akatosh then sealed off the planes of Oblivion, which keeps the Aedra and Daedra from ever walking Nirn again. Alessia's soul was bound to this seal, as Akatosh vowed: as long as an heir of his and Alessia's joined blood sat on the throne of Cyrodiil, and wore the Amulet of Kings, the seal will remain in place and Tamriel would be safe from Oblivion.
What this means is that Akatosh and Lorkhan co-operated.
Whether this was because Alessia walked a middle line between mer and man during her reign is unclear to me.
What is certain is that both deities were not at each other's throats as they normally are