Are you saying that if a meditator can scientifically sort out the specific origin of any particular thought that it will be easier to eliminate?  I’m not convinced of that. 

Way back in June of 2010 I did my first Buddhist meditation retreat. Near the end of 8 days of intensive practice, I entered a mind state where there was no thinking. Upon noticing that, I tried to produce a thought but could not. As I continued to observe the in and out breath, there was an inner vision. I could sense when a thought was about to emerge. I saw a bubble rising up in the heart/chest region. By applying a suppressive force, I could keep the thought bubble from bursting and becoming a conceptual thought. I feel that the normal thinking which obstructs the meditative aim of stillness of mind, is already materialized and claimed as an object. Of course this is a big problem and one must see or sense thought formation before it has matured and been claimed.

Personally, I am of the view that it doesn’t matter what the source/origin of thoughts is. That issue can be investigated after one starves any/all thoughts of attention. When  starvation is applied persistently and with a degree of continuity, thought generation automatically thins. When there is thinning and significant reduction of mental formations then one could investigate the origin of thoughts if one feels that to be necessary.

In Theravada Buddhism, one is told that thought generation is uncontrollable. The formations arise according to cause and conditions. One can train the mind but one cannot control what arises. Whatever comes up and from wherever, one is not to judge or be enamored of it. One is to cut it off and patiently, gently revert to the training method.  

Whether or not one progresses quickly is determined by past actions (karma), past thinking, past speech and of course, intention. 

Thinking is one problem of many.