This was what I wrote in the comment section to Thubten Jinpa's comments:-
Thubten Jinpa wrote quite a long reply refuting a few crucial points stated in the article that referred to a recent incident of him prostrating and making offerings to his Guru’s throne. I was taken aback and was confused by his reply so I consulted a monk friend of mine. He just laughed when I asked him and this led me to ask his opinion on this matter. What he told me blew my mind away because I realized that what Thubten Jinpa said was not true at all!
Contrary to what Thubten Jinpa wrote, he does practice Dorje Shugden. He may have gone underground with his practice but in the monastery, many senior monks know of Thubten Jinpa and that he sponsors Dorje Shugden pujas at Gaden Shartse Tenkhang as thanksgiving for a safe journey after every trip that he goes to translate for His Holiness the Dalai Lama. On top of that, Zemey Ladrang is in Shar Gaden and that means all the monks, students and patrons of the ladrang are practicing Dorje Shugden.
Then, my monk friend paused and he told me that he recalls vividly that an old friend had told him of how Thubten Jinpa first entered the monastery. Apparently, Zemey Rinpoche first encountered Thubten Jinpa in Bylakuppe. It was during this time that Zemey Rinpoche consulted a Dorje Shugden oracle about the boy and Dorje Shugden in trance told Zemey Rinpoche to take care of this boy because he will one day become very famous. In fact, there were many people who had witnessed this.
So, this got me to the point of Zemey Rinpoche and I asked if this High Lama had practiced Dorje Shugden or not. According to Thubten Jinpa, Zemey Rinpoche did not practice Dorje Shugden because he is a worldly protector. When I told him that, he just snorted. He said everybody in the monastery knew Zemey Rinpoche practices Dorje Shugden because the monks at Zemey ladrang would prepare tormas and rituals for a Dorje Shugden puja every month. It is obvious that if everyone in the ladrang is practicing Dorje Shugden, Zemey Rinpoche must have taught them to practice.
In fact, he said he knew of a few older monks and Geshes in Gaden Shartse who would fold their hands with tears in their eyes and talk about witnessing Kyabje Trijang Rinpoche and Kyabje Zemey Rinpoche performing Dorje Shugden pujas together in the old days. He also said that he knew the attendant of the late Choyang Duldzin Kuten and that in the old days; he was told that it is quite normal for Kyabje Zemey Rinpoche to consult Dorje Shugden via the oracle because he trusted Dorje Shugden’s counsel very much especially on important matters. On many occasions, when the oracle took trance of Shugden, Zemey Rinpoche would pose questions and follow through the answers. On top of that, Zemey Rinpoche’s monastery called Yangting Dechen Ling Monastery in Kham, Tibet, continues to practice Dorje Shugden to this day.
Then I asked the monk what he thought of Thubten Jinpa’s statement of Dorje Shugden as a worldly deity. The monk shook his head and said sadly that he doesn’t know why such a brilliant Geshe and student of Zemey Rinpoche would say such things. Zemey Rinpoche is a great student of Kyabje Trijang Rinpoche and everybody in the monastery knows that Trijang Rinpoche is one of the highest lamas of the land and the tutor of His Holiness the Dalai Lama. In Kyabje Trijang Rinpoche’s Sumbum or collected works, especially on the volume of Dorje Shugden, Trijang Rinpoche clearly states that Dorje Shugden is a super-mundane protector or a protector that is enlightened. All of us know that Zemey Rinpoche was a fierce and loyal student of Trijang Rinpoche. So, he must have propagated the same belief in Dorje Shugden’s nature. In fact, if you ask any Geshe in the monastery to debate on the nature of Dorje Shugden, Thubten Jinpa’s views would easily be refuted.
After telling me all that, the monk pondered and he said that he felt that the point of the Thubten Jinpa’s article on the website was actually about Kyabje Zemey Rinpoche being a Dorje Shugden practitioner and so is Thubten Jinpa. With that in mind, much of what Thubten Jinpa wrote in his reply about the Dalai Lama forgiving Kyabje Zemey Rinpoche and seeing him again seemed irrelevant to the original intent of the article. The monk thought that perhaps, it was just a distraction or a smokescreen to cover the fact that he too may have practiced Dorje Shugden.
Having come to this point, I asked the monk what he thought was the reason behind Thunten Jinpa’s anti-Shugden views. He shrugged his shoulders and just said that Thubten Jinpa is well-known to be a hard-line supporter of the Dorje Shugden ban. He wouldn’t say more after that.