So your argument is that it shouldn't stack because because it shouldn't stack.
Pardon me but when cards can be included in deck in quantities of 1-6 it is better design to be able to use cards in quantities 1-6. Flooding and Nightfall are similar and both should be redesigned to the better stackable design. This would come with the companion nerf in order to maintain the balance of the cards.
I think there should be a general thread (in the Design Theory maybe?) about stackable & non-stackable effects and which cards should have stackable/non-stackable effects. I am actually going to make a thread like this, because I have seen pletny of "spamming" in Buff/Nerf sections where the suggestions are about changing a non-stackable card/effect into a stackable one or vice versa. I also should apologize for my utterly offensive previous post.
However, in my most honest opinion I LOVE non-stackable cards & effects because:
1) They encourage more creative deckbuilding; when effects are stackable, you are always like "let's put 6 of this card in our deck in order to grip out the greatest benefit". In other words, when a card is stackable, it just makes almost no sense to include less than 6 copies of it in a deck, reducing the variety of buildable decks which include that card.
2) Non-stackable cards are almost always too powerful if they become stackable; A good example here is SoFre, which is a nice & fairly balanced effect for a shard if used once, but when stacked it is ridiculously powerful, even making it the most broken shard at the moment.
3) There are plenty of occasions where non-stackable cards need to be included even 6 times in a deck; Those occasions include fat decks, stalls, rng-resistant decks as well as counter-resistant decks.
EDIT: I made that thread, the link is
here.