Did you read the article? In Japanese culture, those sorts of exclamations are an integral part of good listening. Its probably pretty hard to just switch that off when you're put in a context with a language barrier
"Being a good listener" has both a practical and a social component. You are referring to the social component ("in Japanese culture..."). The tenets of social interactions in Japanese culture which have been ingrained in speakers of the language to one extent or another. The performance aspect of the act of listening.
antihero is talking about the practical form of "good listening" when they say "that makes you a terrible listener though." That is, what is the function of "listening" in a social interaction? I would hazard a guess that they believe the function of listening is to understand what another person is saying.
And by that benchmark, an individual who is not actually reaching any sort of understanding is a "bad listener" irrespective of how successful they are at performing the cultural/social component of the act of listening.
There's the additional implication that because signaling you are understanding when you are not leads to misunderstanding (which is the antithesis of the intended function of listening), it makes the listener an even worse quality listener than if they were not performing.
Of course, when you're in a specific setting (such as doing science or a police investigation) the other definition can be more relevant.
[1] https://en.wikipedia.org/wiki/Language_game_(philosophy)#:~:....
Reminds me of the "Place, Japan" meme (https://knowyourmeme.com/memes/place-japan). The first panel can have an American not understanding a foreign language next to a disgusted soyjack, and the second panel has a Japanese guy smiling while he doesn't understand a word next to a "clap clap" retard soyjack screaming "amazing listener!"