Here's a screenshot to explain the biggest confusion. The color in the palette shown on the left does not match the color that will be exported (the value on the right).
Also, maybe I'm just stupid, but isn't #FFD600 a valid sRGB color? Why is it a "problem" color that needs to be muted to "fit"?
Just to illustrate how different these 2 particular colors are, here's a comparison:
So the color on the left in this screenshot is the color that is displayed in the palette editor, and then when it's exported for use in Aseprite, the color on the right is what comes out... it's pretty different?