My current theory on why an equal number of feedings does not result in the same plumage: There is RNG involved in whether or not a given feeding counts (or a random amount of color is affected, which is the same thing really). When you get the "New Feathers" message, you've hit a new color. So, starting from Desert Yellow, no matter how many Berries you give your choco, if you stop after the first "New Feathers" (not Plumage, New Feathers, they're different messages!), your chocobo will switch to Ui Brown. Then, from Ui Brown, feeding berries until you get the "New Feathers" message means your choco will switch to Aldgoat Brown.
However, in that first feeding session, you did not have to stop after the "New Feathers" message. If you kept feeding the choco Berries, every new feeding would result in the "New Feathers" message appearing again because the color is already queued to change. But, there is still only a random chance that the Berry will count. What this means is, after the first message, you have no idea if the snacks you feed your choco had any effect or not, but there is a chance that they did and a chance that they didn't.
So, feeding your Desert Yellow choco 3 Berries and getting the "New Feathers" message and then feeding him a fourth Berry all in one feeding session could result in him winding up Ui Brown or Aldgoat Brown. You won't know if that 4th Berry counted until you see the results. You could feed him 7 Berries all at once after the first message, and you could get a Ui Brown choco if only one worked, or Aldgoat Brown if two worked, or tons of other colors if other amounts worked.
If I'm right, then while feeding your a ton of snacks all at once can get you a cool color instantly, it's very random if you'll get what you want or not. To guarantee the color, you will have to stop after each "New Feathers" message, wait 6 hours, and then do the next food. It isn't that the other food is wasted, it's that you do not know if it counted or not.