I have a few nits to pick here...
> scientific understanding of the nature of animals was based on folklore
Popular, pre- or proto- scientific understanding perhaps, but not scientific understanding per se.
> despite a couple centuries of assuming that animals are pure instinct-driven automatons, we have tons of evidence that they are individuals with intelligence, memory, feelings, preferences and even language
These things are not mutually exclusive. The words "intelligence", "memory", "feelings", "preferences" and "language" can refer to purely automatic/mechanical processes, even when we're speaking in reference to humans. There's no real reason why we need non-mechanistic magic to explain the human experience. The two ideas are compatible: animals are conscious, and humans are "just" really complex machines. It's all the same stuff, viewed from different lenses.
> The assumptions of the recent centuries weren't so much anthropocentric
They were, and they still are. Folklore itself is for the most part very anthropocentric.