There's no scientific reason to believe thoughts affect the chemistry at all. (Currently at least, but I'm not betting money we'll find one in the future).

When Scott Alexander talks about feedback loops like bipolar disorder and sleep, he's talking about much higher level concepts.

I don't really understand what the parent comment quote is trying to say. Can people have circular thoughts and deteriorating mental state? Sure. That's not a "feedback loop" between layers -- the chemicals are just doing their thing and the thoughts happen to be the resulting subjective experience of it.

To answer your question about the "thought trap". If "it's possible for simple normal trains of thought to latch your brain into a very undesirable state" then I'd say that means the mind/brain's self-regulation systems have failed, which would be a disorder or illness by definition.

Is it always a structural or chemical problem? Let's say thinking about a past traumatic event gives you a panic attack... We call that PTSD. You could say PTSD is expected primate behavior, or you could say it's a malfunction of the management systems. Or you could say it's not a malfunction but that the 'traumatic event' did in fact physically traumatize the brain that was forced to experience it...