dear john, thanks for your message about this topic and for sharing the extra info.

my comments related to the article above which may not do justice to the method.

diseases are to be addressed in response to their symptoms, with reference to the accompanying circumstances [organon par 18.]
whenever the term "theme" arises, it tends to be a construct of the practitioner/guru; symptoms, provings and the similie law often take a back seat.

john wrote:
"Regarding the opposites in thuja, fixed ideas of a person vs. dual ideas or confusion of identity are clearly opposites and are parts of the cycle of the remedy."
what are the opposites here? what i could speculate [perhaps i am missing it] is that the opposites are-
lack of knowledge about one's identity
'excessive' knowledge about other matters.
many people will say they do not know who they are, many patients will have fixed ideas. these are very often not symptoms of their disease, but aspects of the human condition.

john wrote:
"This method is not simple to udnersrtand until a person understands his whole philosophy and each part of the method including treating the deeper state first and building the whole cycle around that"
also
"It is so much easier to distinguish remedies and to find the deeper state"
this concerns me with reference to the footnote to organon par 1.

john wrote:
"If try to decide between Bar-c and Cal-c always give Bar-c first. Between Bar-c and Hell, always give Hell. first. If not you actually supress the deeper state onlty to return later and confuse the homeopath."
this is not symptom-based work, driven by the patient's symptoms, but a fixed idea of the practitioner/guru. these three remedies have different proving symptoms and characteristics, which alone should determine a choice between them.

some aspects of the method appear to come from the origins of homoeopathy - such as identification of the main complaint as that which is most troubling the patient, and is active disease [ref organon par 7], whether mental or physical. and treatment of the main complaint presenting at each stage. this is symptom-based logical prescribing, and will show better results than sticking to one fixed idea of a constitutional similimum for a given patient.