Any Unit Color will remain its color as long as the Transparent Color slots are indexed to be the Only Transparent colors. An Example is Pure green can also be seen on a Unit as well as be the Transparent color. To do this, you can have the same Green color in the Unit Color Slots and as the Transparent Color. When loading the Palette to the storyboards, colors are applied that come first on the palette. If any of the Green color is transparent on the Unit, it can then be re-indexed by opening the palette, changing the Green Transparent color to Red or another Color not in the Unit. You can then use the color Replacer Tool and change all of the Red color found on the Storyboard to the UNIT Green color on the palette. You then open the palette and change the Red Transparent color back to Green if Desired...or leave it Red
...Alternately, it is best to simply use a different Transparent Color on the Palette in the first place before loading the palette to the storyboards... Yellow, Blue, Green or any Color NOT found in the Unit.
It does not matter what colors the Transparent colors are, it is the slots in which they are found on the palette that makes them transparent.
Edit: If you want the Green Attacks to have more shades of Green that graduate darker on the edges of the explosion you can use a Dark shade of Green as the Background before Rendering. After Rendering, Change all of the Background Green to Magenta, leaving the Graduated Dark Greens with the explosion as you like. You can then Copy and paste those Explosions only to the 1st Rendered Storyboard then make a palette.
You can also manually change the smoke and shadow translucent Shades to any color you want. You need to first have the Green Colors you want for the explosions on the palette. Rendering One explosion with a Dark Green Background should provide the colors you want. Copy and Paste this Explosion onto the 16 Million Color Attack Storyboard in many places then make the New palette. Remove all of those Unwanted Shades of Green/Magenta.
Open the existing storyboard that you have already made a palette for and load the New palette that has the Green colors as well as all other Unit Colors already on it. Use "Nearest Color Matching" when loading this palette to the storyboard.
Open the Palette and Change all of the Shadow (and Smoke shades if needed) to various Pure Colors that are Not in the Unit. You can then use the color Replacer Tool to selectively change only the Translucent colors around the explosions to the Green colors you want by using the Color Replacer Tool to change (Paint) each Shadow or Smoke Shade around the explosions only to any of the Green colors you have in your palette. You do Not change the shadows or smoke shades on the storyboard anywhere else.
This is easy because each Smoke and Shadow Color will be a Different Color that you can easily see. Rainbow of colors that will appear very Colorful and strange
...you then load the same New Unit palette using "Maintain Indexes" and that replaces the Colored Smoke and Shadows back to their Original Colors.
example of a Palette with Colored Smoke and Shadow Shades. The Red Slots would be for the Civ Specific Colors and the Unit Colors.