I think Paul is right with the optical correction statement. To help make the two icon sets stand apart from each other, one being the text color and one being the background color, the text “A” for the background colors are made to be a lighter gray than regular text. This in turn makes the background look a little different.
I think the slight adjustment in Hex Color is simply for appearance in the icon block that it’s shown.
“Design taste” is not about coming up with a strict system (such as color palette) and following it blindly. If designers were doing that, we’d be all designing Procrustean beds
Optical correction is actually a valid design device, and deliberate imperfections are often needed to make things be perceived as more perfect. Here’s a brilliant article about that; it’s about shapes not colors, but the idea is largely the same:
Your comment about Coda having “lack of design taste” is a pretty strong statement. What are you ultimately trying to achieve here? Does the slight difference in tint between the button and the actual color break your workflow in some way or prevent you from achieving a desired doc look? Just curious.