Since the B-side elements already suggest a darker tone, I was considering giving these flowers a prefix like ‘Yamioti’ to mark them as dark-side variants. The difficulty is that Botania itself has almost no themes related to darkness or corruption, so there needs to be a clear in-world reason for how such a ‘fallen’ flower comes to exist.
One possibility is to use the Floral Obedience Stick as a trigger: left-clicking the flower with it counts as ‘punching’, and subjecting the flower to this kind of mistreatment could push it toward a corrupted state. If we follow this direction, planting the flower on stone instead of soil could serve as another form of environmental stress that causes it to fall to the dark side.
A different approach would be to require each dark-side variant to be crafted together with a specific corresponding rune, either directly or via the Petal Apothecary.
Another idea, limited to generating flora, is that if a flower is prevented from producing mana on its A-side for more than a minute, it becomes upset and shifts into its B-side form.
These were enjoyable concepts to explore, so I gathered several possible mechanisms into one proposal.
This is just a small, rough idea, so there’s no need to think too much about it. Keeping it in the back of your mind is more than enough.