I mean, Samus has his DNA in her from him being a blood doner, you could have him be like a phantom/memory haunting the back of her mind in regards to her now knowing she is a Metroid and likely to be outcasted by society because of her being a Metroid now.
The other possibility is that some being ends up getting Samus' DNA after something, they attempt to make what they can with the DNA and somehow, one piece of the DNA she got was in regards to Raven Beak's DNA and whatever creature that her DNA gets used to make gets taken over by Raven Beak or influences that creature.
I mean, look at Other M and how some of the enemies that appear in that game is because Samus' Power Suit had their blood, guts and DNA splattered on it and then the rogue faction took whatever stuff was on her Power Suit and used that to illegally make a bunch of lifeforms, including a clone of Ridley. With how Samus now has Chozo and Metroid DNA and is capable of absorbing the energy of lifeforms and already has absorbed a whole bunch of X-Parasites that absorbed whatever species they infected, killed and replaced, Samus must be a walking DNA factory at this point.