The funny thing is that it/Teridax wasn't mutated, even though Maxilos/Teridax was exposed to the Pit Mutagen.
My theory is that only the bodies of the Mistika Makuta were mutated, but not their energy. Since their bodies were mutated that limited which powers they could use (the same things happens when a Makuta possesses a robot to some extent). Additionally, their mutated bodies would react to usage of certain powers stranegly - such as Krika being forced to drain... was it heat or light? to keep himself from vanishing due to his strong Intangibility powers. Gorast's body might have been mutated in a way that made it dependent on oxygen (hence why Gali could "suffocate" her).
In this theory the Mistika Makuta could have changed bodies if their old one was destroyed - the reason why they didn't do so was an unavailability of suitable bodies in Karda Nui.
As far as I remember the only thing kinda contradicting this theory is that it mentioned either indirectly or directly that the Makuta were now forever stuck in their mutated form... I don't remember the exact phrasing, though.
Another theory is that the mutagen while mutating the Makuta's armor slowly "seeped" through it. That would at least explain how it got to the Makuta's Antidermis in the first place. How it could actually mutate the Antidermis I have no idea, though. We neither know how exactly Antidermis works nor how exactly the Pit Mutagen works and we'll probably never know...