IMO, This has less to do with the verb being used per sé, and more to do with the contrasting of the ideas presented.
This sentence has an explicit subject and an implied agent (someone / something other than the subject that initiates the verbs present), which is a phenomena not unique to Japanese. A similar sentence in English would be:
No matter how much Tom is warned, he never listens, and it’s troubling.
Our English brains interpret this as something like this:
No matter how much Tom is warned [by someone], he never listens, and it’s troubling [to someone].
Could Tom be warning himself, never listening to himself, and thus troubling himself? Sure, but this is not how we usually communicate such an idea. Since the verbs contrast with one another (warn and trouble, vs. not listen), it’s easier to believe that there is another agent, rather than understanding Tom as the sole actor.
In this sentence, it is easier to believe that Tom is the sole actor and agent, since there is nothing to contrast him against.
Other contributing factors to this interpretation:
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As mentioned before, native Japanese speakers tend to refrain from speaking matter-of-factly about someone’s emotional or psychologically state unless there is a strong basis for it (personal experience with the individual, being informed by the individual, etc.)
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「S1 ので S2」is often used in place of「S1 から S2」when the speaker believes the outcome in S2 caused by S1 is fairly obvious and acceptable to the listener (DoBJG pg. 329). It is not obvious that Tom is troubled because he doesn’t listen to people’s warnings. It is, however, fairly reasonable to believe that
whomeverwhoever warned him and was subsequently ignored would be troubled / bothered by his actions.
In my experience so far, a lot of the troubles one has with learning Japanese has less to do with the structure of the language itself, and more to do with the tricky semantics present in almost all human communication that we take for granted in our mother tongue.
Another thing that might help is remembering that pauses / breaks in languages can be quite meaningful. In the example sentence there is a break at the comma, and I usually hear a break after 「ので」when listening to natives speak. These can be clues to help separate the phrases and understand the intended meaning.