Padmasambhava is regarded as an emanation of Buddha Amitabha, the Buddha of Limitless Light, appearing in a variety of forms according to the needs and capacities of those to be trained.
Nyoshul Khen Rinpoche explained the background in an oral teaching he once gave in Paris:
According to the general approach of the Buddhadharma, the story of the historical Buddha Shakyamuni begins from the moment of his enlightenment in India at Vajrasana (Dorjeden), the modern Bodhgaya.
Buddha turned the Wheel of Dharma on three occasions, and finally passed into parinirvana.
Then Padmasambhava came to follow up his teachings, and especially to turn the wheel of the secret mantra vajrayana teachings.
Whereas Buddha gave the fundamental teachings, and opened up the ground, it was Padmasambhava who introduced the teachings of the vajrayana.
Now, according to the extraordinary path of Dzogpachenpo, ‘Buddha’ is actually the true nature of our own mind, our inherent rigpa or pure awareness.
Where did he become enlightened? In the all-encompassing space of dharmadhatu.
From this point of view, events such as his manifestation as the historical Buddha, in Vajrasana, for example, are seen simply as an outer display.
The ‘Primordial Buddha’ Samantabhadra dwells nowhere but in the nature of our rigpa, which is the ‘unsurpassed’ celestial realm of Akanishtha. From out of the space of dharmadhatu he manifests, for the benefit of bodhisattvas, as the sambhogakaya buddhas of the five families: Vairochana, Akshobhya, Ratnasambhava, Amitabha and Amoghasiddhi.
For the beings of this world of ours, he manifested in a nirmanakaya form as the historical Buddha Shakyamuni. In reality, though, he was none other than an emanation of the Primordial Buddha Samantabhadra, who is in our own heart, our own rigpa.
Later, he manifested as Padmasambhava, the eighty-four mahasiddhas, and the ‘Six Ornaments and Two Excellent Ones’, the great masters of India: Nagarjuna, Asanga, Aryadeva, Vasubandhu, Dignaga, Dharmakirti, Shakyaprabha and Gunaprabha.
For other worlds, he manifested in various ways, and for each different species in their own way, appearing as a bird am ongst the birds, as an animal amongst animals, and so on.
Whereas the Primordial Buddha Samantabhadra is our rigpa on an absolute level, the nature or quality of the wisdom of rigpa is radiant and endowed with luminosity, like the sun with its unchanging and unceasing radiance. This quality of the unceasing luminosity of the primordial nature is that Limitless Light or Unchanging Light which we call Buddha Amitabha, Opakme or Nangwataye in Tibetan.
Sogyal Rinpoche - Great Treasure of Blessings.