O manual do POSIX diz isso:
If the -C option is specified, the complements of the characters specified by string1 (the set of all characters in the current character set, as defined by the current setting of LC_CTYPE, except for those actually specified in the string1 operand) shall be placed in the array in ascending collation sequence, as defined by the current setting of LC_COLLATE.
If the -c option is specified, the complement of the values specified by string1 shall be placed in the array in ascending order by binary value.
e contém a seguinte nota
The ISO POSIX-2:1993 standard had a -c option that behaved similarly to the -C option, but did not supply functionality equivalent to the -c option specified in POSIX.1-2008. This meant that historical practice of being able to specify tr -cd%bl0ck_qu0te%0-7 (which would delete all bytes with the top bit set) would have no effect because, in the C locale, bytes with the values octal 200 to octal 377 are not characters.
A partir disso, parece que a opção -c
permite que você especifique valores numéricos representando o caractere ASCII, em vez de usar os próprios caracteres.