When we take refuge in external Three Jewels, inner Buddha and secret Buddha, that means nothing is left behind

All Buddhas can be in three categories: Guru, Yidam and Dakini. And when we say “We take refuge in Buddhas,” sometimes we don’t know which Buddhas. Therefore, we need to have some specific understandings. When you say: “I take refuge in Three Roots,” or “I have special karmic connections with specific Deities,” so you take refuge in those Deities specifically. Then, when we say “Three Jewels and Three Roots” [these are] the external Buddhas, external objects that we take refuge in.
And then the second line says “In the bodhicitta, the nature of the channels, airs, and quintessence.” These three things, the nature of these things, is in the body, and they are also “Buddha”. They are called “inner Buddha”. And then “and in the mandala of essence, characteristic, and compassion”x – these three parts, three qualities of the path [are] the secret Buddha. So when we take refuge in external Three Jewels, inner Buddha and secret Buddha, that means nothing is left behind. If you say only “Buddha”, “Buddha Shakyamuni”, “Buddha Amitabha” then you don’t think about the inner, the essence or nature of things inside. And this is still not enough. That does not include every Buddhas. Therefore, these four lines include everything, every objects that are supposed to be objects of refuge.

 Hungkar Dorje Rinpoche, “Instructions For Dharma Practice”