It’s great to see you both trying out the new color palette setting!
I was able to reproduce the issue with color settings defaulting to transparent, using both rgba(0,0,0,0) and #00000000. I have flagged this for investigation. For now, the practical workaround is to set the initial value to a solid color.
Thanks for the added notes on palette variables in color scheme previews and the + button adding a random color. I have passed that feedback along too.