Been avidly reading this thread while waiting for our seeds to grow, and I'd like to suggest a bit of a theory, see if anyone can test it out.

UNRESEARCHED THEORY:
1) Each fruit has a set value for increasing or reducing color.

2) However, each possible chocobo "dye color" step includes several levels. That is, different combinations of color-fruits can produce the same "dye color" because the full spectrum of colors is not available

3) The "growing feathers" message is given whenever your feeding results in a "step up" or "step down" in visual dye color, that is, what you SEE on your chocobo. (cont'd below)