Definitely he's not just some random fanfic writer. He's made a lot of the offical lore in the past. But in the Imperial Library site where the text about the Thalmor is posted, it says his writings there are "Unofficial lore documents gathered from forums".
The main word being "unofficial". I just can't accept that the Thalmor want to destroy the whole universe just based solely on unofficial forum posts, even if they were created by a talented author who used to work for Bethesda years ago.
The in game lore has definitely gone against some of his ideas. For example, it should have been Lorkhan, not Akatosh, who visited the dying Al'esh and made the Amulet of Kings. What it comes down to is it might not be canon, though certainly the Thalmor plans make perfect sense when you consider the fate of the Dwemer, but which is most interesting to you.
That's the reason it's 'lore', not 'history'. Even the in game books are written by flawed, prejudiced, possibly egocentric authors, and should be taken by your character with a pinch of salt. If there is something you don't want to believe, simply don't believe it. It's a single player game, as we are told so often, but in a way it's a single player world as well, open to your interpretation.
Just remember, though Nirn looks pretty Earthlike in places, and it's men look like us, we are dealing in the background with a world in which the laws of physics are dead gods, the sun is a hole ripped in possibility through which the magic of a primordial 'heaven' flows, and visiting a shrine in the wilderness will make even the greediest merchant give you better prices. Mundane concerns are not always on the agenda.