The Mammon Machine wasn't destroyed until it's destroyed in the Black Omen in 12,000 BC.
Are you saying the dustructed state its in when you first appear and see it in the main hall where QZ is? Or do you mean after you destroy it in the PD? Come to think of it, there is no evidence to say it even was physically in rubble again after the u destroy it n the PD. Of course it probably just when down with the Black Omen and got vaporised.
Also, maybe when u get 'thrown' into the MM, the MM is actually 'reconstructed' from its rubbled state and powered up unbelievably due to the FF and Lavos' connection with the BO.