The following seemed to be a rather fair assessment of Pabongka Rinpoche's more controversial stands that I have extract from Wikipedia:-
Pabongka Rinpoche's position on other Tibetan Buddhist schools
Although he was a Gelugpa Lama, Je Phabongkhapa respected the four schools of Tibetan Buddhism and discouraged sectarianism. In Liberation in the Palm of Your Hand, he said:
"Abandoning Dharma is, in the final analysis, disparaging the Hinayana because of the Mahayana; favoring the Hinayana on account of the Mahayana; playing off sutra against tantra; playing off the four classes of the tantras against each other; favoring one of the Tibetan schools—the Sakya, Gelug, Kagyu, or Nyingma—and disparaging the rest; and so on. In other words, we abandon Dharma any time we favor our own tenets and disparage the rest."
Je Pabongkha also said that Padmasambhava (the founder of the Nyingma school), Je Tsongkhapa, Atisha, and Buddha Shakyamuni were all one holy being, not four separate mental continuums.
Pabongka Rinpoche was at times at odds with the 13th Dalai Lama over Pabongka's supposed antagonism toward the Nyingma lineage. His advocacy of the Dorje Shugden Protector practice is also now criticized by some in the Tibetan Buddhist world. Von Bruck, however, says that Pabongka's Shugden text "does not say that only Gelukpa teaching leads to liberation, but calls Tsongkhapa's teaching the highest and the essence of all teachings. But this is traditional parlance and not an exaggerated exclusivity."
According to academic David Kay, in an account that has been much disputed by Gelugpa scholars: "As the Gelug agent of the Tibetan government in Kham (Khams) (Eastern Tibet), and in response to the Rimed movement that had originated and was flowering in that region, Phabongkha Rinpoche and his disciples employed repressive measures against non-Gelug sects. Religious artifacts associated with Padmasambhava – who is revered as a "second Buddha" by Nyingma practitioners – were destroyed, and non-Gelug, and particularly Nyingma, monasteries were forcibly converted to the Gelug position. A key element of Phabongkha Rinpoche’s outlook was the cult of the protective deity Dorje Shugden, which he married to the idea of Gelug exclusivism and employed against other traditions as well as against those within the Gelug who had eclectic tendencies."
According to Kay, "His teaching tour of Kham in 1938 was a seminal phase, leading to a hardening of his exclusivism and the adoption of a militantly sectarian stance. In reaction to the flourishing Rimed movement and the perceived decline of Gelug monasteries in that region, Phabongkha and his disciples spearheaded a revival movement, promoting the supremacy of the Gelug as the only pure tradition." Buddhist scholar Matthew Kapstein echoes these remarks, writing, "There has been a great deal of sectarian dispute among Tibetan refugees in India. Much of this has its roots in the works of Pha-bong-kha-pa Bde-chen snying-po (1878-1937), whose visions of the Dge-lugs-pa protective deity Rdo-rje shugs-ldan seem to have entailed a commitment to oppose actively the other schools of Tibetan Buddhism and the Bon-po."
However, most Gelug Lamas strongly dispute allegations against Pabongka's supposed wrong-doing. Some say that Je Phabongkhapa’s popularity made others jealous, serving as the basis of many rumors of sectarianism on his part against other Tibetan Buddhist schools. Responding to this allegation, Lama Zopa of the FPMT has said that criticism of Pabongka "because he practiced Shugden, making him out to be some kind of demon" is misplaced because he:
"wrote incredible teachings on sutra and tantra; on Heruka, Tara Cittamani and many other topics. All these amazing teachings were written purely from his experience. So it’s impossible that he can really be some kind of evil being, as those extremists accuse him of being. There’s no way he could have done the negative things they say he did."
Regarding Kopan Monastery giving up Dorje Shugden practice, Lama Zopa also pointed out:
"This was done for His Holiness (The Dalai Lama). This does not mean that Pabongka Dechen Nyingpo, His Holiness Trijang Rinpoche, and His Holiness Song Rinpoche have made mistakes. It does not mean they are wrong. Nor does one have to look at the protector as evil. For us ordinary people it is difficult to judge, because we cannot see these lamas ’ minds. Another side of the teaching is that it is mentioned that the protector (Dorje Shugden) is an Arya Bodhisattva, a manifestation of Manjushri. So, then, there is also the risk of our creating very heavy karma in that context (by criticizing or abandoning this practice)."
Geshe Kelsang Gyatso also rejected the rumors that Je Phabongkhapa was averse to the Nyingma tradition, saying:
“Je Phabongkhapa had great devotion for Je Tsongkhapa. Je Tsongkhapa praised Padmasambhava, so it is impossible for Je Phabongkhapa to show disrespect for Padmasambhava, impossible.”
Kyabje Zong Rinpoche, a high ranking Lharampa Geshe and Abbot of Ganden Shartse, said in his teachings:
"Kyabje Pabongka was also an emanation of Heruka Chakrasamvara, but degeneration of the times and jealousy of ordinary beings have made it difficult to become aware of his tremendous qualities. There are many biographies of Kyabje Phabongka that make his realized qualities very clear."
Kyabje Zong Rinpoche also explained the importance for Gelugpas of developing faith in the Gelugpa lineage passed down through Je Pabongkha and his principal disciple Trijang Rinpoche:
"Kyabje Pabongka passed all of his lineages to Kyabje Trijang Dorje Chang. He often said this in discourses. The purpose of this detailed exposition is to affirm the power of the lineage. If we lose faith in the lineage, we are lost. We should remember the biographies of past and present teachers. We should never develop negative thoughts towards our root and lineage gurus. If we do not keep the commitments after having received teachings, this is a great downfall.”
Pabongka Rinpoche's Position on Bon religion
Regarding Pabongka Rinpoche's attitude toward the non-Buddhist Bön religion, he said that "The dharmas of Boenpos, tirthikas, and so forth are non-Buddhist and should not be taken as our refuge." In his famous work Liberation in the Palm of Your Hand, he calls it an "evil system", "false dharma", "not worthy of being a refuge", "plagiarized", and "invented". Although the Bon religion was originally highly hostile to Buddhists, Je Phabongkhapa never advocated intolerance towards them: "Boen is not a refuge for Buddhists; it is not worthy of being a refuge. All the same, Buddhists and Boenpos say things to each other out of attachment or hostility, and this hardly makes for honest debate. It is vital that you should know the sources of the Boen religion." To support his claim that Bon is not a fitting refuge for Buddhists, Je Phabongkhapa quoted several Buddhist scholars, including Milarepa who said, "The source of Boen is perverted Dharma. A creation of nagas and powerful elementals, it does not take one to the ultimate path."
