Garchomp LV.X's Restore says to put the chosen Pokemon on your Bench 'as a Basic Pokemon', as stated in the attack text. Ampharos Prime is still considered a Stage 2 Pokemon for the sake of powers such as Staraptor SF's Poke-Body "Protect Wing", but it is considered Basic (and therefore unevolved), and therefore its attacks could not hit Mewtwo LV.X.
