I mean, Janeway even becomes aware of her own soul,
What's that got to do with destiny? They're entirely separate metaphysical concepts.
It has to do with the fact that there is a metaphysical part of the universe. There is something bigger and deeper than just the material.
That doesn't remotely answer the question. Just because destiny and the soul are both hypothetical metaphysical concepts, that doesn't mean they're directly intertwined, or that any given metaphysical model of the universe is required to include them both. Since we are talking about fiction here, there are countless different ways in which the imaginary physical or
metaphysical laws of a fictional universe could be formulated. A work of fiction that presumes the existence of something that can be called a "soul" within its putative reality is not necessarily presuming the existence of destiny. The two concepts have nothing to do with each other beyond both falling into the general category of metaphysics.