Being focused in the present is awesome, but the fact that we have the ability to pay attention on things other than reality is not a problem, but in fact essential to the health of the mind (our "spirit" if you will). Imagine if all your circumstances sucked and all your mind could focus on was reality...
Secondly, this essay sounds like he's much more inner-focused, as I know that I rarely have these "flow of thought" and self-conscious moments that he calls being "submerged again by the flow of thought"... If you asked me at any moment what I was thinking, I would tell you "nothing"... Obviously I'm thinking something behind the scenes, but my focus is just not on my thoughts when I'm doing. So my own personal thought-life does not confirm this silliness.
Then again, I'm very extroverted and rarely focused on my own thoughts -- maybe it's my "clearly false" Christian religion, or the fact that I've been a runner for 20+ years which is essentially meditating on present experience (pain), but I just have a strong natural tendency to focus on the present experience rather than my own thoughts.
Even if you're looking at this under the domain of science, I would still argue that the ability of humans to cope with present circumstances is directly correlated to their capability to focus upon that which is not the present. (i.e. thinking joyful thoughts, etc.).
That little essay is pitiful, talk to "robg" here on YC if you want to hear from a Neuroscientist who has a better respect for this domain of mind and spirit. The way this guy just starts with a bunch of assumptions and blasts away at all potential truth in less than 1,000 words gives me no respect for his method of thinking.