I don't really understand your objection. It seems to me that you're really objecting to either Asperger's or autism as a category, I don't understand how you can define it without some form of generalization, just by looking at individuals.

I also don't think the author treats these thinking patterns as deficiencies; in fact in the original link, he also notes where they give a definitive advantages.

Regarding the other comment, I always thought that Asperger's was a certain subset of the autism spectrum. Maybe it is not useful as a category, but maybe it is, I am not sure. But I don't really care that much how we categorize things; the reason why I find the list useful is that lot of the described behaviors in it (1) I see in my coworker (and partly also myself) and (2) have a common explanation. Two other points. First, I also don't think OP claims that people on the spectrum lack empathy, but we would have to be more specific, there are different types of empathy. Second, the author of OP is by his own admission also on the spectrum, so I don't see how his experience is in any way inferior to the experience of the other people on the spectrum, which is being suggested as a literature here.

I don't think this kind of generalization is stereotyping; if I can correctly generalize and predict the way you think out of the myriad of your individual preferences and behaviors, it is useful for you as an individual. Stereotyping is something else, it's attributing traits to others based on some classification of them, rather than their own behavior.

Specifically, regarding my coworker, I don't attribute these thinking patterns to him based on whether he is on the spectrum (I don't know, and I don't care), that would be stereotyping, but rather I observe a lot of the patterns in him, and therefore I think that he is on the spectrum. But maybe, because of everybody on the spectrum has a different experience, it is not useful to think about it that way.

That however doesn't contradict that the thinking patterns described in the OP share a certain way of looking at the world, and as such might be useful, regardless how we call it.

In particular, I can easily see my coworker getting fired (or contributing to it) for what he did yesterday (it was pretty scary, TBH), and I don't want that (luckily, I was the only witness). That's what could easily happen if we just naively assume him being neurotypical, that is, without looking at his individuality. And that's where I disagree with you that generalization like OP did is always harmful. In this case, general understanding of his thinking patterns by his coworkers might actually help him and others to avoid these problems (the feedback loop of negativity) in the future.

In other words, you could use the OP's list correctly or incorrectly. Correct would be to look what behaviors are in a particular individual, and use the common explanation as a possible guide. Incorrect would be to assume that since you see some of them in an individual, they will also have other traits from that list. It seems to me you're really objecting to the incorrect usage, which is a logical error, but it doesn't really invalidate the explanation that is behind (at least some of) the items in the list.

Addendum: I find meta-amusing that you write:
"The author leans heavily into stereotypes and treats autistic people as a separate species with uniform deficiencies rather than individual people."

Isn't that something you would exactly expect from somebody thinking like a person with the traits in the list, who is trying to "logically" (and perhaps in a bit of a black/white fashion) understand the world, without much regard about social mores?