The author and most people here are using "modal" with a very common popular meaning where the word is a short form of "modal window".
You are confusing it with the much less common but technically accurate meaning in UI. So you are just confused by terminology, and even though it would be better if people stick to unambiguous words, they are talking about something well defined enough that discussing terminology isn't useful.
Right. And, in my opinion, we get exactly the bad UI described because it became common to conflate "modal" with "overlay." That's the way the UI kits implement it, and as the author states, it makes people reach for that because it's what's available.
You are confusing it with the much less common but technically accurate meaning in UI. So you are just confused by terminology, and even though it would be better if people stick to unambiguous words, they are talking about something well defined enough that discussing terminology isn't useful.