Color Palette

On the color palette it is not related to the stackup. The color palette only pertains to the selection of available colors that you can use to assign a color to an object.
That would be the "Available Colors" choice under The Color Dialog which is accessed via > Display > Color/Visibility.

Basically it is just a selection of colors to use. There can be confusion with the color palette in that one might think this would also hold the design colors. For example say you color the pins blue and your etch is green. and then you save the color palette as something for use later on another design. Loading the color palette into your new design wont change the colors of the pins or the etch.

On colors and such things it's easier to look at it from exporting those colors for use on other designs. Assume you have everything setup from a color perspective and you wish to use these colors on a new design. To do this go to export > Parameters. In there choose Color Layer & Color Palette and export to a file name of your choice.

This creates a file that contains the assignment of colors to objects and also the actual palette of colors that were used. To load that file on a new design. go to file > import parameters.

The main difference between loading the .col file and one based on a parameter file is a parameter file gives you more options. With the parameter file you could also include things like your design settings. From the perspective of the palette they would be the same.

Best regards.