I've almost got it. Turns out there's no need for a palette correctional factor when editing after all, but it is still needed to get an approximation of what CT sprites are supposed to look like in Tile Molester. I say "approximation" because Tile Molester may be incapable of viewing compressed CT sprites by simply loading the correct palette in the ROM. The player characters can be viewed correctly, but the NPCs don't seem to match up perfectly with their palettes, even with the palette correctional factor. Or at least I couldn't view Schala correctly. There may be some condition that applies specifically to compressed sprites.
Can anyone think of an example of an NPC or enemy sprite that has a full 12 colors? (Magus doesn't count because he's always uncompressed). That would seriously alleviate some of the concerns I have right now. I've got enough knowledge to take care of the Ark anyway, because it's less than 12 colors.