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.