Nature's Aura v:1.12.2-1.5.1
Forge: 14.23.5.2781

The book reads: "During this process, it can neither be stopped, nor harvested."
I break the flower and it stopped (though it wasn't harvested.)

"Cannot be harvested" means that it won't drop.

Not the harvesting. The stopping

If you smash your coffee machine with a hammer, it will stop working, despite the fact that it might not have an off switch.

But the box said it wouldn't. I suggest removing the "stopped" comment to avoid confusion.

How would a thing that's literally destroyed not stop working? It's very clearly implied in my opinion.

Ok, let me rephrase. Why are you saying it cannot be stopped?

Because it solves the implication that, maybe, with a redstone signal or a second eye, you'd have the ability to stop it from releasing its aura without destroying it.

But you don't.