Regarding:
   
  "...but this doesn't work because the .mode tabs isn't separated from
the regular SQL.
  Could someone point out how to accomplish this?"


If I understand correctly, all you need to do is write the desired
commands out to a text file, then either direct stdin to the text file,
or use the '.read" command. 

With Windows, FWIW, I have more luck with .read  , e.g.
    Sqlite3 NLSY.db ".read MyFileOfCommands.sql"

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