Sure the thoughts can influence your chemical state. Scott even provides an example. Suppose you become so engrossed in your weird idea you start to lose sleep over it... Or start to feel anxious about it.

At some point, your induced stress will cause relevant biological changes. Not necessarily directly.

PTSD indeed is likely an overload of a normal learning and stress mechanism.

The core thing is, am I really in control of my brain, at a fundamental level? If my thoughts are the result of electrochemical reactions, which everywhere else in the universe follow normal deterministic (even if stochastic) physics... How does thinking actually change their result? The unsettling conclusion is that it doesn't. The thoughts are the result of the reactions continuously in progress, and any sensation that we are a actively making decisions and guiding the process is simply an illusion created by that very same process. I.e. there is no free well.

Under that view, the bipolar feedback loop example disappears. The engrossing or psychotic thoughts are not driving the chemistry, they are the chemistry. The whole thing is just a more macro view where you see certain oscillations play out. If the system ultimately damps itself and that "feels like" self control, it was actually a property built into the system from the start.

It's chemicals all the way down