Thoughts may be be represented in unconscious forms (written down, for example), but thinking is a conscious activity. As far as I know, there is no consenses, scientific or philosophical, about how consciousness works or what it even is. See all the competing theories: dualism, panpsychism, emergence, supervenience, reductionism, etc.

"The conscious sense of self emerges from loops of self-referent symbolic representations."
Therefore this is just one speculative theory among many. As such, it just proclaims this without proving it. How could just a bunch of representations be conscious (have subjective experience)? Even if that is possible, which seems dubious, it remains a mystery. Maybe someday we will understand consciousness, but we are not anywhere near that yet.