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If I may quote Nāgārjuna, one of the greatest exponents of emptiness (Mūlamadhyamakakārikā, XXIV/14): "That to which emptiness is possible, everything is possible." The fact that our mind, and for that matter all phenomena, is empty and dependently arisen allows for self-development and growth. Thus, for the philosophers who assert buddha-nature to be the emptiness of the mind, free will and self development are indeed possible. The fact that sentient beings are by nature inclined to be free and liberated reinforces the notion of free will.
This buddha-nature resource, like many other endeavors, is an effort in the direction of helping people recognize their compassionate nature and capacity for enlightenment however deeply entrenched their materialistic and negative habits may be. Like a precious statue buried under the earth for centuries can be dug out and its value properly appreciated, we can also bring out our innate qualities of compassion and wisdom through the right exposure, education, and experience.
To take the refuge vow is to accept the Buddha as the main teacher, adopt his path as one's spiritual path, and follow his disciples as spiritual companions. Thus, one is advised to abandon those teachers and paths contradictory to what the Buddha has taught.
Worshipping local deities and propitiating them for temporary help or protection, such as making offerings to the territorial deities, does not necessarily contradict the path the Buddha has shown. Thus, Tibetan Buddhism permits the worship of territorial deities. However, it would be considered wrong to take refuge in the worldly deities with regard to one's long-term spiritual goals of liberation and enlightenment because the deities are believed to be themselves trapped in the cycle of existence. Having said that, some territorial deities are considered enlightened buddhas and bodhisattvas by their believers.
From the perspective of buddha-nature, all sentient beings, including worldly deities, have the capacity for enlightenment, even if they are not already enlightened. Thus, they also can manifest wisdom and compassion and eventually become buddhas.
Buddha-nature as a nature of awareness/consciousness can certainly be studied scientifically. Projects through the Mind and Life Institute and similar initiatives are making inroads into such research into the mind, and there are several dialogues going on between scientists and Buddhist teachers. I suggest you follow the works of Thupten Jinpa, Alan Wallace, John Dunne, Richard Davidson, and Daniel Goleman, et al. for new findings and possibilities.