Was Je Phabongkhapa a spirit worshipper?

[From Je Phabongkhapa, root Guru of Trijang Rinpoche:]

The One Hundred and Fifty Verses of Praise says:

Take refuge in whoever does not have
And never will have, any shortcomings
And in whom resides
Every aspect of all good qualities.

If one with such a mind exists,
Take refuge in him,
Praise him, and venerate him.
It is right to abide by his teachings.

In other words, when we think of how to distinguish between what should be a refuge and what should not, we will want to take refuge in the Buddha, the teacher of Buddhism, in his teachings, and in those who abide by his teachings. The average worldly person seeks refuge in worldly creatures—spirit kings, gods, nagas, spirits, and so forth. Non-Buddhists seek refuge in Brahma, Indra, etc., but these themselves are beings in samsara, so they are not fitting refuges.

Who then is a fitting refuge? From the Seventy Verses on Taking Refuge:

Buddha, Dharma, and Sangha
Are the refuge for those desirous of liberation.

That is, the only refuge is the Three Jewels: Buddha, Dharma, and Sangha. But if we do not identify these three properly, we will not take refuge purely. We are not critical and so pretend to be Mahayana knowledge-bearers, yet when things go wrong, sickness comes and so forth, or when we have some important work to do, we seek refuge in worldly Dharma protectors, in spirit kings, local gods, etc.—we carry an armload of aromatic wood for a smoke purification and rush off to the shrine of any deity having a statue in the neighborhood. Inwardly we should entrust ourselves to the Three Jewels; instead we cling to spirit kings. The external reality indicates our inner state. We may have actually gained admittance to a monastery, but we do not even qualify to be Buddhists, let alone Mahayana knowledge-bearers.

Nagas, spirit kings, and others do not have these three qualities: omniscience, love, and ability. They don’t even know when they are going to die. Normally they are categorized as animals or hungry ghosts, and their rebirths are inferior to ours. No matter how badly off we are, we are still human. What plan could be worse than to seek refuge in them? Forget about protecting us from samsara and the sufferings of the lower realms, or even giving us temporary help—they may do us great harm instead…. Non-Buddhists make Brahma, Indra, Shiva, Rudra, Ganesha, and so forth their refuge. This is an improvement on the above, yet these gods are still not liberated from samsara and the lower realms so they cannot protect other beings. But Buddha, the Teacher of Buddhists, is not like these. Praise to the Praiseworthy says:

You proclaimed, “I am friend
To you who are without protection.”
Your great compassion
Embraces all beings.

Teacher, you have great compassion,
You have love; you act by your love.
You are diligent, you are not lazy.
Who else could be like you?

You are protector of all sentient beings;
You are a kind relation to all.

Buddha has three magnificent qualities: omniscience, love, and ability. Not only do spirit kings and so forth not have even a portion of these good qualities, but also the sum of the good qualities of worldly refuges, gods, nagas, and the like, cannot rival even the good qualities of a single Buddhist shravaka stream-enterer. (Je Phabongkhapa, Liberation in the Palm of Your Hand: A Concise Discourse on the Path to Enlightenmentpp. 354-355, © 1991, 2006)

Once you have taken refuge in the Buddha, you should not do things like seeking refuge in worldly gods. There are even now some monks who, if driven to desperation when things go wrong, will grovel abjectly before the idols of worldly gods. They are a disgrace to Dharma practitioners. As I have already told you, by taking [a second refuge] you cast yourself out of the ranks of Buddhists, because you destroy the refuge vows in your mindstream. All the same, it is all right to offer ritual cakes, perform smoke purifications, make burnt offerings to gods, nagas, spirit kings, and so forth, if you merely invoke their help in Dharma matters. However, you must not take refuge in them. It’s like giving someone a bribe and asking them to help you: you don’t have to take refuge in them. (Je Phabongkhapa, Liberation in the Palm of Your Hand: A Concise Discourse on the Path to Enlightenmentp. 380, © 1991, 2006)