One set of rubbers displaced won't cause a rattle. You only need one set in place to stop the fins contacting each other.
There's really nowhere else for them to go - if they're not in place they'll be sat in the recess under the alternator. If they're slightly displaced then the alternator won't slip into place like it should, you'd have to fight it on.
On mine, the rubbers had completely disintegrated leaving the fins to smash each other to pieces and there was still no discernible rattle.
A rattle from here is more likely to be either a dead/dying bearing or the dog bolt/cup nut loose.
Of course, you could have installed the alternator with the cup misaligned, meaning the fins are all up against each other and the rubbers are doing nothing - imo it still wouldn't rattle though.........