The primary philosophy behind building these sets up like this is because, honestly, I dont feel like the Pokmon TCG has a lot of story-driven sets
Part of fantasy is the idea that you're coming to a world that is fundamentally different than your own
The once noble Brimaz, Blight of Oreskos has been brought into Phyrexias fold, rewarding you with Incubator tokens with every Phyrexian spell you cast, and Ixhel, Scion of Atraxa, a true Poison Counter commander, dedicated to infecting every player it can with Phryexias venom
Many proxy-friendly pods continue to allow it given its iconic status, and it remains fully legal in Legacy and Vintage
While you may think that destroying the target of the mutating creature would cause the spell to fizzle, the mutate spell on the stack just goes onto the battlefield as a normal creature instead