Well, there's the fact that it's Abed who introduces the concept, and who then ushers us back into the "regular" timeline. It's Abed who muses that the roll of the dice will create multiple timelines, and Abed who brings us back. It's also Dark Timeline Abed, in the credits sequence, who declares that his timeline is the "darkest" timeline and decides to start wearing an Evil Spock Goatee -- something not likely to happen if Dark Timeline Abed actually believed his timeline was the timeline; it sounds more to me like the depiction of Abed's imagined alternate self in his own mind than something any version of Abed would actually think.
And then, of course, a few weeks ago, Abed "encounters" the Dark Timeline Abed while in the Dreamatorium--and somehow Dark Timeline Abed just happens to have gotten ahold of a space ship and has been somehow monitoring events in the Prime Timeline? It's highly implausible.
So it all seems more likely to me that the alternate timelines were Abed's musings rather than "actual" alternate timelines.
