The way I am given to understand it, throughout ALL incarnations of the Transformers, there is only ONE Fallen. He exists in all realities simultaneously. For example, the Fallen who was in the second movie, is the exact same entity who might show up in the Shattered Glass universe, or in a future attack on the beast wars universe.
So yes, there is always going to be the possibility that The Fallen might show up, working with Megatron against Optimus Primal... and reference the Michael Bay movie. And it's totally canon.
Edit: Yep, he's considered a multiversal singularity.