OK, so I have done the great disambiguating, bringing the examples to the other tropes.
All that is left is: All Myths Are True. Are these examples a pattern worth YKTTW'ing, or just a jumble of things that would warrant only a disambiguation?
I noticed that His Dark Materials is listed in both the normal AMAT and in Fantasy Kitchen Sink, as well as left on that sandbox page. I'm not really familiar with the series, though, so I have no idea which actually applies.
Mage: the Awakening: 1 is probably the trope being subverted
Dungeons and Dragons/Eberron: 1
The Elder Scrolls Oblivion: Maybe 1b if you really squint
Chrono Cross: ZCE, possibly an aversion to 1
Thunderstruck: Subversion of 1a
Abe Kroenen: Subversion of 4, which therefore might be considered a subversion of one of the others
Wayward Sons: 1a, sort of
Tasakeru: 1 or 3
Roswell Conspiracies: 3
Sleeping Beauty: This is the opposite of the title, so I don't think it should count. See below.
Stranger in a Strange Land: This is basically one agnostic character. Probably shouldn't count.
Myths of Magic: Explicitly false.
The Elder Scrolls Morrowind: This is an "exception" where everyone has a different myth they tell and only one of them is true; Sleeping Beauty should be considered an exception of this type. Not sure what trope it's an exception to, though.
Fire Emblem: One particular myth turns out not to be true and a cover for a different myth. So, sorta 4?
The "Other" Example: Aversion of The Legend of Chekhov and inversion of one of the above, in that everything they encounter turns out to have an associated myth, followed by numerous myths turning out not quite to be true as is
I just looked up what trope 1b is: Prophecies Are Always Right. However, all the examples in this list are Playing with a Trope, specifically some entity arranging the prophecies' existence in order to further their own ends (though The Elder Scrolls Oblivion remains confusing regardless). That may be YKTTW-worthy as well.
Given the existence of A Mythology Is True, you would expect All Myths Are True to be that But More So (assuming you consider "myth" and "mythology" to be equivalent terms), so basically some combination of 1, 1a, and 2b, maybe 2a as well.
IIRC the only myths in Harry Potter are the Chamber of Secrets and the Deathly Hallows, both of which turn out to be true. Other than that it belongs on Fantasy Kitchen Sink.
EDIT: Ok, done editing now.
Thinking about it, I think the 1b examples wound up with this trope as a sort of "lite" form of One Myth To Rule Them All, in this case, One Myth To Explain All the Prophecies. (See my explanation above.)
Also, I think it's the generic 1 case that sounds like Legend Of Chekhov, and I suspect most of those aren't actually used as Chekhov's Guns, or Septimus would have moved them there.