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Great list @Q726kbXuN that you compiled at glyph_counts.txt. Very interesting to see the frequency of unusual characters in NYT crosswords.
I dropped your list as-is into the code, but removed:
So this is apparently every non-Latin-1, non-emoji character ever used in a NYT puzzle. A value of 'None' in the table causes the encoder to insert its own replacement. I put in conversions where I could think of something decent, but clearly this is more art than science so please feel free to edit. :)