I honestly agree that the IDW backstory for Nightmare Moon was stupid and should’ve been better thought out. I don’t remember much about the Sirens so I can’t say anything about them.
I take it that the “evil” Celestia you’re talking about is the one from the Reflections arc? Or are you referring to Daybreaker? If it’s the former, then I don’t consider the existence (or even the mere idea) of an alternate reality to be impossible.
What other draconequus-like creatures have popped up besides Cosmos and Eris? (Trying to remember) a As for other brands of ponies, specify? Side note, I might be forgetting something or misremembering so sorry in advance.