Actually, not
all of those mythical foxes are of the trickster variety, as can be read
here.
Kyubey having the nine tail imagery in that scene where Sayaka becomes a Puella Magi prompted me to research into nine-tail fox legends to see what it might say about Kyubey.
And lo and behold, there are indeed malicious nine-tail foxes, but also ones that "...put the fox in a more tender position, whose simple desire was basically to seek a companion to share the human experience of love and happiness...".
Really, nothing concrete was said about Kyubey by the nine-tail shadow imagery.
It was just SHAFT being SHAFT, imo.
No, they're not. Not at all.
A supernatural or magical being is often fundamentally different from a more naturalistic alien being. They're different conceptually too.
Furthermore, many Star Trek fans absolutely hate it when Star Trek goes into a more mystical or supernatural direction, as they did at times in DS9.
Likewise, pure fantasy fans would
not have been amused if Lord of the Rings had been resolved by an ET-esque alien swooping down in his flying saucer to destroy Mordor.
For a lot of viewers, these differences matter.