I’m happy! Great news… ))
I’don’t think the bugfix refers to your original complain, the bug affected the color-display directly after a color-change in the color-palette-setting.
Regarding your complain: The pad-color can’t be set independently from the copper-color. And it will not come back in v6.0.x (and also not in v7 - as there is already a feature-freeze announced for the development of that version).
You could try to change the transparency-slider for copper-tracks and/or for Pads in the appearance-manager–>objects-tab (on the right side).
There was already a discussion on that topic: PCB Editor 6.0.8 pad color, but with only 2 complains since januar 2022 (release of v6.0.) I think most users can live with the developers decision. It’s just a matter of habit.