So is Keith Baker's eberron book on DMs Guild canon, or is the upcoming WotC hardcover?
I'm not familiar enough with Eberron to say. Do Keith Baker and WotC disagree on what the story of Eberron should or would have been?
I do know if it came down to a call between Ed Greenwood contesting what was considered canon and WotC, you'd probably have a great majority side with Greenwood. Normally Greenwood is more relaxed and has just about anything as Canon though, as I think he considers additions by others essential in creating a joint existence for a game world.
For literary and other purposes...it normally defaults to the original creator as the baseline canon, even when others create more extensive universes and such. Those other creators can have their own canon, but it's not the baseline for everything else to build off of.
For example, Tolkien and CS Lewis have both had other companies create multiple canons specific to those companies. Since it's an RPG board, Middle Earth has had MERPS which had it's own Canon. However, it is Tolkien's original words and writing which take precedence.
Much of this is because a license can switch companies, owners, writers, and many other things. When this happens it is not uncommon for that Company's Canon to change. Thus, in the example of MERPS, the current owners of the Middle Earth and LotR RPG rights do not have to adhere to the MERPS Canon. They are expected typically to hold to the original canon from the Books of LotR, the Hobbit, and to a lesser degree the other works that came later attributed to Tolkien himself, even though those works were not especially endorsed by Tolkien, they were supposedly written or at least approved by him even if not adopted wholescale. Thus, you can see Canon from one license tossed wholesale in favor of a new canon and things change from one person running the show to the next.
However, it is RARE for the original creator's canon to change (more especially after they are dead...but it normally does not have that many changes even while they are living though they may add quite a bit to it...Lucas has twerked the canon for his own SW canon himself, but it's core has essentially remained the same).
Thus, if looking at media works, it's normally the creator's canon which is considered official, with various unofficial canon's by the various license holders (if the work is popular enough to reach that point and is licensed out) as that specific owner's canon, but not the official canon that would be utilized by others if they ever came to own or control the license. Basically the Creator's canon is that which is seen to be the base upon which all other canon's are built off of.
