If anything, it’s probably the opposite. We actually know that smart-atom abilities can be “given” to people and other races in the universe have been getting good at making superhumans with that technology. Humanity itself is getting pretty close. Eve is a smartatom superhero; it’s only that she manipulates the environment, not herself, and she does it consciously, not subconsciously like a Viltrumite. Humans are creating near-Viltrumite supes like bulletproof.
I don’t have a citation… but I’m pretty sure it’s said somewhere that Viltrumites haven’t always been this OP; that they modified themselves, then naturally selected until they became that OP. So I wouldn’t be surprised if Viltrumites used to be actual humans before they did all of that stuff to themselves.
I imagine universe hopping. Like Viltrum was colonized by humans from another timeline. The issue with this is that Viltrum exists in multiple universes.