Are there parallel or alternate universes in Magic? Such as… - Ravnica-2 where each guild is a 3-color combination - Theros-3 where gods are artifacts - Jace (from Vryn-5) and Jace (from Vryn-7) meet each otherPlanes can have alternate universes, yes, but it's not common. The three planes we know have them, or
had them, are Dominaria, Rabiah, and Tarkir.
Dominaria's you can see in the set Planar Chaos, there's one where Mirri strikes down Selenia instead of Crovax, one where the Odyssey legends are color shifted, one with different primeval dragons with the wedge colors instead of shards, one where Serra was obsessed with Sphinxes instead of angels, that kind of thing. It's possible these are all the same AU, I'm only listing them as different, we don't have more stories about them than the basics. In the Planar Chaos novel we also see "Ice Age Phyrexians" but don't learn more about them.
Rabiah is refracted 1,001 times, which in the diegetic reason there are no legends in the set. Each refraction is different in some way, although it's not really explored much except in Taysir's backstory for the five versions of him that fused.
Tarkir is more recent, but we've see the Khans timeline, which doesn't exist anymore.
lonedm:
What about the comics? Does that count?
Uhhhh it's complicated?
For most franchises with a 'multiverse', separate continuities are normal and are different worlds within the multiverse.
In Magic parallel realities are generally divergent timelines that get made real, for one reason or another. The Boom! comics
could be considered an AU, but they aren't structured like other Magic parallel realities. So... it's an AU in the real-world sense of things but not necessarily in-universe.