That’s not where your learned words are stored, as you said, and so it is likely to be replaced if the en-US dictionary is updated in a later patch release. (It’s also not simply a plain text file; the hunspell format is actually pretty complex to allow the smallest amount of entries to match the largest number of possible words.
To move your custom wordlist, check out this thread:
All references to Scrivener 2.9 are to the 3.0 beta, so it should still work the same.