I don't think you're wrong (or right) but I think there could also be more variety to the structure of monsters. Something like, the monsters who infected us and Oscar might not have been Numbered, they might have been descended from the Numbered. Ella may have been afraid of that one monster because it is something that Makes Monsters. Basically, the theory goes
12 numbered come down/up. They Make some monsters.
Monsters make superhumans which either themselves turn into monsters, or stick around, maybe joining H.E.R.O. or other such organizations.
Superhumans who Turn can then turn others into monsters.
Those 2nd generation monsters are weaker, but still trace their lineage back to the original twelve.
This process can repeat, and the things that infected us may have been 2nd, 3rd, 4th etc. generation. We were still infected by two different trees, but they were small branches, which the spooky thing in the dead end demonstrates are nowhere near as powerful as the originals.
Also, I don't think the numbers that they are directly tie to their power. I think it's more likely thatthe first was literally the first, but may be weaker than some of the others, or there might even be a complex edlritch horror rock paper scissors going on, like in Eternal Darkness (Muscle beats mind, Mind beats magic, Magic beats Muscle, but 12 ways instead of 3)
Also, I like your theory for artificial evolution. I'm not sure if we know that the 12 in H.E.R.O. all had Artificial evolutions, just that Klaus did. It also sounds super recent, so I think they might Just be Wrong, and they might be able to evolve more. Like how we used to think Electrons were the smallest things.