It's hard to control. Healthy user bias is always a possibility in studies of this kind.

Chocolate will likely have some positive effects and some toxic effects. A mechanism for potentially beneficial effect is explored but we don't know the net effect.

Most plants are toxic to most animals. Chocolate can kill a dog. Is it doing some damage to humans as well?

If you enjoy chocolate then go for it. It's probably not that bad for humans. I wouldn't put too much stock in speculated health benefits of it.