You can start to create your own plank theme.
If you just want a dark theme to use right away, look at https://github.com/ChildishGiant/elementary-dark-plank. It fits very well with the default dark theme on eOS.
I'm pretty sure you've linked to the right answer: Plank's badges are separate from notification center, and they have to be implemented separately. However, you might consider adding a wishlist item on the launchpad.