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This issue may extend beyond just unicode.upper() and unicode.lower(), but it's very clear with these two methods, at least.
For example, consider DESERET SMALL LETTER EW. On a UTF-16 build, calling upper on a string containing this doesn't change it to the capital variation (DESERET CAPITAL LETTER EW):
>>> u'\N{DESERET SMALL LETTER EW}'.upper() == u'\N{DESERET SMALL LETTER EW}'
True
It can also be seen that this isn't even recognized as lower case:
>>> u'\N{DESERET SMALL LETTER EW}'.islower()
False
With a UTF-32 build, however, the expected behavior (ie, the behavior one would get for a code point in the BMP with small and capital variations) is provided.