Subsetting works by using the CMAP table (of type BMP) in the font, it maps unicode character codes from the Basic Multilingual Plane (BMP) to glyphs. If your font does not use a BMP type CMAP table to map unicode characters codes to glyphs then it wont be subset correctly.
IIRC BMP tables dont cover the private use area of unicode, so I doubt subsetting will work for such a font.
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