"What is striking in the case of Alan Wallace is that the position he appears to present in his book regarding an atman-like (yes!) consciousness that underpins all experience (and reality itself?) is strongly influenced by Dzogchen, a practice and philosophy found in the Nyingma school, but a view that is rejected vehemently by Tsongkhapa, the founder of the Geluk school.... The Prasangika-Madhyamaka philosophy of the Gelukpa has no time at all for any kind of primordial or pristine consciousness, which, correctly I believe, it regards as a return to Vedanta. Much of Tsongkhapa’s polemical writings are taken up with rejecting this practice and its philosophical corrollary of gZhan sTong ('Other Emptiness').... It has always struck me that the “Mind and Life” dialogues between the Dalai Lama and scientists have suffered from a strong, though often unstated, bias towards Dzogchen and its reified and idealistic notion of atman-like consciousness. Many of the leading Buddhist voices at these events have been Dzogchen practitioners: the Dalai Lama himself, Matthieu Ricard, and Alan Wallace. (On another note, this kind of view is becoming normative of much 'Eastern spirituality' in the West, particularly under the influence of the neo-Vedantist Ken Wilbur and his followers/admirers — it is hardly surprising that Wilbur practices and endorses Dzogchen).... I believe that by positing an atman-like consciousness, Dzogchen (and similar teachings found in Chan/Zen – and even in the Theravada Forest Tradition) are implicitly abandoning the a-theism of the Buddha and embracing another theos called Pristine Consciousness/ the One Mind/ the One Who Knows etc."
Compare with Reynolds (aka Vajranatha) on Dzogchen:
"Our conscious thought process is changing from moment to moment; it is as fleeting as reflections seen on the surface of the water. But the Nature of Mind is outside and beyond time and conditioning.
"Everything is part of a single continuous reality.
"Level 0 or what is called in Buddhist terminology Shunyata. This term literally means 'emptiness.' But this does not mean just nothingness or mere absence. Rather, it means the pure potentiality for all possible manifestations....this level is referred to as the Nature of Mind.... Level 0 is accessed directly through Dzogchen practice."
He notes that both traditions, Nyingma and Bonpo, assert that Dzogchen did not originate in Tibet but rather central Asia, and "was brought to Central Tibet sometime before the seventh century from the previously independent country of Zhang-zhung, west of Tibet, and more remotely from Tazik (stag-gzig) or Iranian speaking Central Asia to the northwest." Early Bon teachings came not from Buddha but from Shenrab Miwoche, based on the Causal Ways which were "considered to be dualistic in their philosophical view."
The Nyingma "tradition claims that it originally came from the mysterious country of Uddiyana to the northwest of India. Therefore, it appears most likely that it is to the Indo-Tibetan borderlands of the northwest that we should look for the origins of Dzogchen.... Zhang-zhung had extensive contacts with the Buddhist cultures that flourished around it in Central Asia and in the Indo-Tibetan borderlands. Just to the west of Zhang-zhung there once existed the vast Kushana empire which was Buddhist in its religious culture. It was an area in which Indian Buddhism interacted with various strands of Iranian religion-- Zoroastrian, Zurvanist, Mithraist, Manichean, as well as Indian Shaivism and Nestorian Christianity.... All this suggests that certain trends within Yungdrung Bon...actually do go back to a kind of syncretistic Indo-Iranian Buddhism that once flourished in the independent kingdom of Zhang-zhung."
That latter of which were also dualistic in their philosophical view. Hence this was not the Indian Buddhism of Nagarjuna but rather a system that tried to include the Indian Mahayana by adding and mixing it with these other, Indo-Iranian Buddhist views. A distinctive brew for sure, but questionable as to its strictly Nagarjunan interpretation, about which Tsongkhpa was wont to wax poetic and polemic. And about which Garfield and Thakchoe assert the same dualistic tendencies.