Save options are done - including the disabling of alpha bit depth the specific compression type doesn't support. As well as writing the header for the saved file.
Since Photoshop doesn't seem to let file format plugins do much with Photoshop itself, I'm in the middle of tracking down a good library for color reduction, for saving to Indexed (paletted) formats.
Hopefully I'll have a fully functional plugin, for at least CS6 for Windows x64/x86 by the end of the weekend.