Bradylama
So Old I'm Losing Radiation Signs
The super mutants can't maintain the culture of the Unity without the Master, which is why the Nightkin are so thoroughly screwed. Dumb super muties can always follow smart super muties with the brain power to find a new purpose for the mutant diaspora, but the Nightkin need stealth boys to help manage their psychosis and all of their interests revolve around that addiction.
You're massively overthinking things bringing up the tunnelers and stuff like this. I said that ghouls and super mutants aren't humans "per se" because for all intents and purposes they are still human; it's just their genetics that have been scrambled. Practically speaking there's no difference between a super mutant and a mule. Mules aren't viable themselves, yet as a hybrid they're also not a horse or a donkey. Tunnelers are irrelevant because they have no ambitions and can't hold a conversation. They're dumb animals who will likely never leave The Divide. I know Ulysses says they could threaten the outside world since their tunnel networks are constantly expanding, but we're probably never going to see them again anyway.
The important thing about the Vault 4 natives is that they're people who can reproduce like normal humans can and pass on what are presumably radioresistant genes. Those mutants are the most desirable breeding partners in the entire wasteland. They should be able to pick and choose whoever they want from the surface to expand their population and form settlements on the surface, but they're fine with staying underground despite everything they knew about the NCR. They're a big huge deal for the setting and they're wasted on a bad joke.
Also as an aside - You say that ghouls and Super Mutants are so different as to not even be considered humans. While it's true they might pass outside of the human species, neither can represent a species in and of themselves: Neither can reproduce themselves by organic means or pass on their genes. They're mutants in the truest sense of the word, evolutionary dead-ends.
Another viable, speciated human mutant I thought of: Trogs from Van Buren, as opposed to the ones from Fallout 3. I don't know if we're every explicitly told how they reproduce, but it seems pretty clear from context it would have to have been organic.
You're massively overthinking things bringing up the tunnelers and stuff like this. I said that ghouls and super mutants aren't humans "per se" because for all intents and purposes they are still human; it's just their genetics that have been scrambled. Practically speaking there's no difference between a super mutant and a mule. Mules aren't viable themselves, yet as a hybrid they're also not a horse or a donkey. Tunnelers are irrelevant because they have no ambitions and can't hold a conversation. They're dumb animals who will likely never leave The Divide. I know Ulysses says they could threaten the outside world since their tunnel networks are constantly expanding, but we're probably never going to see them again anyway.
The important thing about the Vault 4 natives is that they're people who can reproduce like normal humans can and pass on what are presumably radioresistant genes. Those mutants are the most desirable breeding partners in the entire wasteland. They should be able to pick and choose whoever they want from the surface to expand their population and form settlements on the surface, but they're fine with staying underground despite everything they knew about the NCR. They're a big huge deal for the setting and they're wasted on a bad joke.