Regarding the mind and what it can affect
The question that you are referring to is worded in a way that I think is leading to the confusion. The question in the title is "Can the mind affect the brain?" but in the question body the final question posed is "Does [a thought producing a tear] not contradict the (physical) law of cause and effect?". 

The answer is yes to the title question: the mind can affect the brain. The answer is no to the question posed in the body: it is not a contradiction of the law of cause and effect because the mind is a physical entity.

So you are exactly right, that the two are mutually interactive.