There's also an artbook that came with the "multiverse edition".
(Photo credit: https://www.youtube.com/watch?v=AAke-M4gyHo)
There's also the Prima strategy guide that may have names in it. (I can't say how many are in that one because I don't have it.)
What I mean is: If a name is shared across multiple official publications (down to the exact spacing and letter casing), it most likely is canon*.
(By the way, original filenames may not always match what's on these artworks/books. As Tom said, filenames were placeholders at first. Printed material should always have more weight.)
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*Now, regarding canonicity: I do know that the artbook says the following:
"Incidentally, many of the names here are not the official names of the creatures, merely what I imagined Trace would nickname them, being a physicist and not a taxonomist."
So, what does that mean? What are the official names then? How canon are the names in the book?
To me, it just means that, in universe, "official" names have not been decided yet. If "Red Snailborg" were to get an "official" name in universe, it would need to be like: something in latin, that would sound legit (like Cyberneritimorpha rubeus) as if it had been named by a "real" taxonomist (in the lore).
The names that Trace has given can be seen as the official vernacular names of the creatures (because Trace was first to name them, and the only scientific papers documenting them were written by him).
The purpose of a wiki is to document what exists. Not leave readers wondering why the names here are different from the most frequent ones seen elsewhere.
It doesn't mean that we can't rename a creature (if the name Trace gave is really really bad). But we need a pretty solid reason to do so. I'd say: on a case by case basis, and based on these guidelines: https://en.wikipedia.org/wiki/Wikipedia:Naming_conventions_(fauna)
If you believe a given name should differ from one given by Trace, please explain why you think so (in great detail), and one by one.