>>56060651Manaphy prevents DAMAGE from attacks. It blocks things like Radiant Greninja or Scream Tail which have the ability to hit benched pokemon with their attack damage. It does not block EFFECTS from attacks that place damage counters on the board, like Dragapult Ex or Sableye. It may seem arbitrary but it's an important and explicit distinction for the sake of game balance. It means there isn't a single catchall shield for bench, and it allows the potential for manaphy to be dispatched from the bench by means of effect.
Frankly at this point in the game, Manaphy is basically only run because Greninja is so potentially devastating. Jirachi does the opposite and blocks effects that place damage counter from attacks (from basic pokemon), but not direct damage.