Each location (including towns) has two NPC palette assignments, each corresponding to two NPC palettes, for a total of four NPC palettes per location. You can edit the palette assign!ents in FF4kster, in the graphics portion (the second window) of the Map Info editor. I believe palette assignment 0 has the red and blue townsperson palettes, and assignment 1 has the purple and a generally unusable green and blue palette (don't know if it's used for anything, but it seems to be a terrible choice for any NPC).
Chocobo forests have palette assignments 2 and 8. The yellow and white chocobos use assignment 2, so you can change the 8 to whatever you want. Only the black chocobos would be affected.