Taking refuge in one deity is taking refuge in all Buddhas
In a very general way when we say “Take refuge” then [the question is] “Take refuge in which?” We take refuge in the Three Jewels. In that case it is about enough and this is a very general way of saying. But if you say specifically? When we say we take refuge in Buddha, then [the question is] which Buddha? Buddha Shakyamuni? Generally speaking we take refuge in all Buddhas. But specifically, when you say “I take refuge in Guru Rinpoche, or Amitayus, or Amitabha” we have some specific practices [of those Deities]. In that case, we still take refuge in all Buddhas, but specifically take refuge in that specific deity, [because] the Deity we are taking refuge in represents all Buddha. That’s one way of understanding when we say about taking refuge in the Buddha or Three Jewels.
Hungkar Dorje Rinpoche, “Instructions For Dharma Practice”