I think he makes the mistake of assuming that every person has a similar life experience to his own. I've read his biography, and apparently he was extremely intelligent and acted like an adult from a very young age. It could be that he hated being seen as a child and saw himself as a fully functional adult in a transitioning body.

In everything he says and does there is an extreme single-mindedness: his extremely strict free software and privacy related ideas show this. I think he applies a similar single-mindedness to a clearly nuanced situation, namely that of conscent. The nuance of power dynamics and coercion probably don't play a role in his experience and therefore he ignores it. This results in the very wrong and dangerous opinions stated in the article.

I am not saying this to excuse any of his opinions, this is just my interpretation of where it might come from. It's sad that the people around him are seemingly unable to educate him on these topics, but I believe it might be the same stubbornness that made him the proponent of the Free Software movement that is causing him to not mentally grow on this specific topic. It's a truly unfortunate situation, but one that should not be ignored and people who oppose him because of these opinions are right to do so.