The closest thing we had to a Elseworlds or "What If..." scenario is Hearts of Steel (Although it was later made canon in the IDW 2005 continuity) Are there other examples of Elseworlds stories?
Transformers has never really had a main continuity like DC or Marvel, so stories that take place in their own continuity are pretty much common place.
Because of how fragmented TF continuity is, what counts as an 'elseworld' isn't always easy to define. It's not like in Marvel or DC where there's a 'main' continuity and a bunch of 'what-if' stories or reinterpretations that are deliberately meant to stand apart from that. In transformers, moreso things are meant to stand on their own, alongside all the other stories. Still, these might be closer to what you have in mind: - The recent Transformers 84 one-shot comic - The Dreamwave transformers/gi Joe crossover - The Devil's Due transformers/gi Joe crossovers - The Mars Attacks / Transformers crossover (or any of the Evolutions or Deviations sub-imprints) - The New Avengers / Transformers crossover... Sort of - The Beast Wars gathering/ascending comics... Sort of You'll notice a lot of crossovers.
I will say that I'd like an official streamlined G1 continuity based on Beast Wars being the future end of it; a clear timeline of events for future Neo-G1 storytelling and quasi-sequels to be based upon. Then, and only then, can we truly proceed with Elseworlds mentality - which, BTW, was created with the idea that a multiverse doesn't exist following The Crisis of Infinite Earths. (I actually rather enjoyed the post-Crisis/pre-new 52 Modern Age DC comics - it was a great place to jump in on.) Until then, it's just another thread in the Transformers Multiverse, of which I've grown quite tired of as it feels too much like a story crutch now.
Um... you got that a little backwards there. Transformers have ALWAYS had a main continuity. What they lack are stories that take place outside of that. DC and Marvel have had MULTIPLE main continuities just like Transformers has. There isn't really any such thing as one MAIN continuity over all. The main continuity usually refers to whatever continuity we're currently following or talking about. Elseworlds would refer to alternate continuities that don't really have a main story line of their own. Things like Shattered Glass. There's technically two different SG continuities that currently exist. G1 SG, where the characters mirror events from the main G1 continuity and Animated SG where the characters mirror events from Animated's continuity. There's never been a SG universe where SG was the main continuity. It's always been an elseworld universe that crosses over with the main universe it's trying to mirror. Oddly enough Supergirl could be considered both a main universe and an Elseworlds Universe. It's a main universe because she actually has her own show. She's not a character who only appears for crossovers with the Arrowverse. But she's also technically Elseworlds because she's not actually from the same universe. The same could be said the other way around. There is no one main universe... there's actually two main universes that we follow... possible three because it's not clear at this point how Black Lightening fits in. They're main universes because we're actually following their story through their entire journey. The Nazi versions however we only saw glimpses of in crossover events. That's the only time we ever see that Earth. Same with Jay Garrick, 90's Flash, or Robert Queen as the Green Arrow. We've only seen glimpses of those universes, we don't have a full story, those are elseworlds only not main universes. There are a lot of main universes in Transformers. G1, RID1, UT, Bayverse, Animated, Prime, ect. But there aren't really a lot of elseworlds other than Shattered Glass. There's also apparently a location on Cybertron where the barrier between universes breaks down allowing characters from different continuities to interact with each other. Some of these are main universe characters others seem to only exist in the Hub between universes. So I guess this could be a elseworlds story. There's a story that takes place in the Hub where Megatron keeps getting confused as to what yellow kid appeal character he's talking to. He's called Bumblebee, Cheetor, and Hot Shot at different points in the story.
Basically every continuity is an Elseworld in this case. Prime, IDW, Armada, and G1 Starscream are all vastly different conniving personalities. Prime Arcee, g1 Arcee, and IDW Arcee would probably not share social circles. IDW Magnus would not see eye to eye with RID Magnus. Etc.
In the end, I blame Hasbro when they announced in 2000 at Botcon that every new series would be rebooted and self-contained but still Transformers "like Final Fantasy". That was a very dumb move because it came out of belief that modern kids couldn't follow the story set forth in 1984. You know, how kids in 2000 obviously couldn't understand how Bruce Wayne became Batman after his parents were murdered in an alley because that was written back in 1939? Hasbro seriously underestimated the power of their franchise (and the kids that followed it) for years...and ended up with the fumbled Unicron Trilogy (story wise) and the ten different continuities that followed it including the botched Aligned continuity.