Default palettes undergo far more scrutiny than secondary, non-canon palettes. The reasoning still holds water. It just means that we screwed up and didn't take visibility into consideration when making the brown palette. "Welp, we didn't think about the brown palette. Guess we should throw standards out the window!"... doesn't make much sense does it?
If the answer that would satisfy you regarding that is "OH SHIT, YOU'RE RIGHT, MAYBE WE SHOULD CONSIDER CHANGING THE BROWN ONE FOR BETTER CONTRAST/VISIBILITY", then there you have it. However, it's not like we set out to improve all of Val's palettes here. We were forced to look at specific palettes, and make very specific changes to meet criteria we didn't get to choose. We needed to make sure the change made sense in every way possible within those criteria, and we wanted to spend only as much time on it as we absolutely needed to BECAUSE AS YOU MAY HAVE NOTICED, GUYS, WE HAVE OTHER IMPORTANT WORK TO DO. We're pretty frustrated that we had to spend any time on this AT ALL, because it means it takes that much longer for us to bring you the stuff you all donated for, and the money we get paid to get it to you is WORTH LESS.
Fun fact: Because of this change, you will get to have Fukua earlier. Had we not been forced to make this color change to Val, you wouldn't be getting Fukua until the Eliza patch comes out.
Fun unrelated fact: render loves using Caps Lock.