What this says to me, is that when the darkness is within the people they have immunity from whatever causes the problems, and when it is removed they start to slowly devolve
On the topic of Diabolos’s explanation, the Ultimania states that after removing the darkness, this is what made the Kuluu susceptible to evolution into the Tonberry. While I don't know if the Darkness makes them immune to evolution (it may, I’d have to look into it), it was a prerequisite for what happened to those people. The Emptiness and Promathia’s essence is actually a really convoluted topic that I won't get into here, but suffice it to say, the Emptiness seems to be the source of human cognitive sophistication. It is why enlightened races and beastmen are “people" and animals are not, in Vana’diel lore. This is what Diabolos was referring to when he mentioned how the Emptiness was essential to their survival, lest they become like the Tonberry.
A group of Zilart in an area, some became 1 of the 5 races and the others that were not "contaminated" became beastmen.
The Beastmen did not come from the Zilart. They apparently evolved over the course of Vana’diel’s history. This is actually explored in tVR and confirmed when Garazu-Horeizu mentioned that Chaos does not attack the enlightened races out of his loyalty to the Zilart.
The explosions didn't just release the darkness, it also allowed the protocrystals to form.
The Protocrystals are actually Zilartian creations. They harvested vast, practically limitless stores of crystal energy from the Mothercrystals and then isolated them by element. This is what formed the 8 protocrystals. Yve’noile states this in Rise of the Zilart.