I would agree with you if this were a venture initiated by publishing companies, but this is something pushed by Amazon and the franchise(s). In this deal they are cutting the publishing companies, and the authors, as a middleman of sorts in this scenario. And I would think name recognition could swing in the favor of self-published if they had the backing of the franchise.
In your Stargate example, at least how I see it could happen, is that MGM no longer uses Signet Books to publish their books and uses their resources to spotlight online, self-published stories they deem acceptable. This gives them more control than working with a publishing company and established authors. Lower quality but more control.
Edit: Also, it just occurred to me that "Vampire Diaries" was on the list of authorized fan fiction. "Vampire Diaries" is based off of a series of books. That by itself hints of an end run.