Ballos' Final Words

Defeating the core either breaks or interrupts the power of the red flowers/crystal. My running theory is that the red flowers are tied to Ballos' magic (and magic-derived insanity) given that they can be controlled by the crown. I suspect that the Core represses Ballos' magic, and the red flowers are formed from a bleeding of said magic, like an overflow on a dam. When the core was destroyed then the magic probably returned to Ballos' control.

 

I thought that the red flowers didn't really have anything to do with Ballos or the Doctor?

The Doctor uses them to make the Crystal, and they're apparently also referred to as Demon Flowers, which ties in with the naming of the Demon Crown. The Demon Crown can control the rabid Mimiga that the Demon Flowers create, so they're probably both linked to Ballos.