If you lock a perfectly normal six year old child in a basement/closet (environment) for four years, that doesn't make them become autistic. Yes, they will most likely have all sorts of issues, however, autism won't be one of them. It's a developmental disorder, and usually appears in young children, regardless of whether or not they've suffered some kind of trauma. My point was that this horse's problems are most likely related to being locked in a stall for most of his life, and yes, that may have resulted in biological changes. Autism still isn't something that you can "cause" in the way this article is referring. This horse has socialization issues, but as far as i can tell from the article, he's still a neuro-typical horse. He still wants to interact, with her, and with the other horses, even if he does apparently have trouble "reading" the social dynamics.
I don't think you can separate biology and environment all of the time. However, that also doesn't mean that you can always link them together.
My main issue with this whole thing (not directed at you Sum!) is the number of paypal links on that one website. I frequently donate to causes that I care about, and horses in need/in kill pens are a big one for me. With all the issues that this horse has though, I don't see the need for any major medical care. He appears to be under "control", as sound as he'll ever be. So why the donations? If his owner/trainer/whoever can't afford the basic hay and grain bills, should that become our responsibility just because he happens to be a rescue horse? If that's the case, well, all of my animals are rescues, so hand over the cash.