I think what you mean to say is you didn't intend to say that. Whether or not you actually did say that is another matter entirely. In this case, the majority of your post seems good. But the big bolded sentence that grabs your eye first seems to be implying that there's something wrong with an organization that uses Windows.
I mean, imagine telling someone you don't like their cooking and then saying "The fact that you use margarine instead of butter says a lot." You're not directly saying anything bad about them personally, but most likely they're going to take it as a roundabout way of saying "Real cooks use butter, but you use margarine. Therefore, you're not a real cook."
"But the big bolded sentence that grabs your eye first seems to be implying that there's something wrong with an organization that uses Windows."
So what if he did? By the time you've reached that point you really ought to have figured out the entire post is a subjective opinion.
Here, I'll say it too: I don't want to work for an organization that primarily runs Windows by default. I don't have to justify it rigorously scientifically. Nor am I saying there are no skilled Windows developers in the world. In fact my company has quite a few in it ("some of my best friends are Windows developers", ahem). Nevertheless, I do not want to work for a primarily Windows company. I do not like Windows software culture.
He can say what he wants, is the thing. When you reply to a "why didn't you take the job with us?" feedback request, you can be as succinct/diplomatic as you think is appropriate. The OP did the same.
I mean, imagine telling someone you don't like their cooking and then saying "The fact that you use margarine instead of butter says a lot." You're not directly saying anything bad about them personally, but most likely they're going to take it as a roundabout way of saying "Real cooks use butter, but you use margarine. Therefore, you're not a real cook."