This quanta is not random! In the notes it says that the quanta generated matches your mark.
Ah! I misread it then. I thought only quanta from "Crumble" matched the mark.
In that case, you are right that the upgraded version's production should probably be dropped to 1 per turn.
Although, he does note that a deck is limited to 6 of these per deck.
Also, it is probably a good idea to let players know that the quanta matches their mark. Otherwise most would probably assume it to be random.
One other amusing option to balance the upgraded version would be something like:
"Generates 2 quanta per turn.
Quanta type matches mark.
May crumble (self-destruct).
Crumble: Generate 6 quanta"
In other words, the tower may crumble at random (maybe something like 20% to 50% chance each turn).