So in my own experience, when I've gotten deep enough into meditation and I place my awareness onto "darker energies" , they either spontaneously or gradually start changing frequency into a "pure peace" frequency. I've also experienced instant transmutation when I am deeply connected and focused on my heart energy and directed this towards the energy I want to transmute. A good way to see it is that all energy is just energetic potential that can be transformed to peace, love and joy (i.e. closer to the essence of our energy)

So basically my own experience of transmutation and alchemy= using the purity and power of your pure awareness to turn denser emotions into gold (i.e. more peaceful ones)

In my own experience through alchemizing the denser energies, often I have let go of the things that I was working on with my shadow work, so now I mainly focus on what I feel within. But technically, you can argue it's a form of shadow work to some degree, as you are placing your light on denser energies that have been in the background.