You're operating on the assumption he's just coming up with all of this now. The Thalmor have been around for over a decade, we're just seeing them crawl out of the woodwork for the first time now. Sure, we don't know for a fact that Bethesda considers the Altmeri Commentary On Talos "canon," but deny MK's authorship is absurd. Do you really think he hasn't discussed this with them?
(Also, again, there is a nod to it in Ancano's dialogue).
Personally I prefer to hold that "canon" should be determined by Bethesda-the-ever-shifting-collective-of-authors-who-created-Tamriel to Bethesda-the-nebulous-corporate-entity, but whatever floats your boat, man. Just let people suspend disbelief in whatever they like, rather than trying to shut people down for their ideas and trumpet the One-Divine-Canon-Truth that Bethesda themselves have always avoided like the plague.
I respect your personal preference, but honestly, I don't think having a universal standard is at all necessary. I don't know if you've ever been to /r/teslore on reddit or The Imperial Library Storyboard, but those communities hold strongly to the idea that canonicity is subjective, and it hasn't hurt discussion at all. If anything, it's blossomed a wonderfully helpful and creative group of people. So long as people are honest about their sources (i.e. "according to [X In-Game Source]" "according to this Temple Zero doc" "I think it would make sense if") and bring a sense of good-faith to discussion, it works perfectly well.
Something to keep in mind when contemplating Skyrim's civil war is that the game is designed so that the "good" side is whichever one you pick, i.e. which one's heroic and which one's evil depends on your point of view. As a result, the game is seeded with plenty of evidence to support either view- claiming stuff like "such-and-such NPC hates the Stormcloaks, which PROVES that Ulfric is an evil baby-eating monster" rather misses the point; there are plenty of other NPCs who think the opposite. Everyone in this game is biased.
Personally, which side I support depends on how long its been since I played the other side. Right now I'm on the tail-end of a Stormlcoak period, but I've been feeling the urge to follow Hadvar. Biggest trouble is I haven't actually finished the Civil War on either side yet (I tend to get bored before I can); I love them both, but can't decide which one should be my "first."
Keep in mind that, while the Thalmor did manipulate Ulfric (and the Empire, I might add) into starting the Civil War, that doesn't mean that A) Ulfric and the Stormcloaks don't still have good reasons for what they're doing, or B) they actually want Ulfric to win. They want the war to continue for as long as possible, draining resources and manpower from the Empire.
Either side winning is very bad for them- you either have a newly reunited Empire with a whole army full of combat-tested veterans or a fully independent Skyrim that owes absolutely nothing to the Dominion. (the terms of the White-Gold Concordat give the Thalmor a lot of influence over Imperial affairs, which is why all this mess started; if the Empire had just made peace with the Dominion but didn't allow the Thalmor so much access to its territory, it's likely none of this would have been necessary)
Ulfric is not a sleeper agent; he is not a Thalmor toady; when they say "uncooperative to direct contact" they mean they can't control him by walking up and saying "Do this." Unlike with the Empire, if they want to manipulate Ulfric they have to do it through indirect means. (such as getting him pissed off enough at the Empire to start a rebellion) Ulfric is as much of an "asset" to the Thalmor as Tulluis- they just try and control him through different means. (as they try and control everyone)