yes, two ways.
first, somewhere in the script editor are functions that define the color numbers for each part.
these functions can be edited to change to other color numbers, either directly in the default scripts or by adding scripts that are designed for that (for example the Luna Engine).
Second, although that is a bit problematic for other reasons, you can edit the color palette in the windowskin picture. This however changes the color for everything that uses the same definition and can cause strange effects if you make a wrong color replacement there.