Read the first page only, and skimmed the last page so sorry if it's posted before.
To counter the monkey theory (a good one btw) I had an idea from reading MurderMachine's theory.
There has been a theory for awhile now that Argotha (sp) or the civilization under the earth has played a part in the zombie story. I suggest you go read his topic if you are confused.
My idea was, perhaps once the missiles hit earth, it destroyed Argotha, which has been abandoned for awhile (it's people left earth and never returned) so once they are gone, ofcourse other life forms will thrive anywhere a human can, so these evolved "monkeys" became night creatures, giving them the large eyes and nimble body structures.
It's my idea that these Denizens were to new inhabitors of Argotha and became large in numbers. Once the missiles hit, Argotha was destroyed by the lava from the earths core, pushing them to the surface. This is how I think they were discovered and experimented on.
So to the theory of having them tested on I can agree, but to say they were engineered could be debatable, and I feel my idea would be a good mirrored topic. Once the zombies came, the town was abandoned and in the midst of the chaos, the denizens escaped, to breed and now inhabit the earths surface.
The eyes are obviously because they lived underground, this is a very common trait in most creatures who live in dark or underground areas. The fact they come out of the ground tells me they have superior hearing (like tremors if you remember that movie) to compensate for their sensitive eye sight.
If you look at their legs you'll notice the structure is wrong for a monkey. The noise they make doesn't resemble a monkey in the slightest. And the fact they don't come from the trees, or that they cannot climb at all is another hint that perhaps they are not from monkeys.
So to me, they were an alien creature from Argotha, pushed from their homes from Maxis's missiles, some were captured and once the zombies reached green run, escaped when their captors were dying. From that, we are now enemies to them.