Would future versions of Quicktime or other ALAC coders be able to do a good job on this kind of file?
If I'm going to be able to make claims about the audibility of this kind of filtering, I'll want it to be convenient to keep and play multiple copies of my music. I don't think I even have a media player that can handle FLAC files and output 24-bit audio.
Given a 24-bit stream, ALAC stores the lower 8 bits completely uncompressed while applying the compression to the high 16 bits. The "wasted bits" bit in the frame header indicates whether that uncompressed block of lower 8 bits is present or not, but it is generally the opposite of FLAC's use of the same term.
AFAIK your ipod is just truncating to 16 bit (probably without dither) so you might as well just keep the 16 bit version on your player, and the store the 24 bit one as FLAC.
Do the ALAC format and Quicktime library support storing just two extra bits uncompressed at the end of each sample? If so, it might be desirable for XLD to add a feature "truncate to n bits before encoding", so that it could know to call the encoder with the right settings.