Not with the base shaders available in the editor.
However, when you bring your effect in the final game engine, you can override that with any custom shader you like.
For instance, if you're using Unreal4 with the PopcornFX plugin, when importing the effect, you can override any of the shaders with custom ones, so you can use this color-remap logic in an Unreal4 shader and bind it to the appropriate renderers in your effect.
If you're using an in-house engine, you'll have to see this with your graphics programmers, as it might depend on how they did the rendering integration.
Customizable shaders will be exposed in the PopcornFX v2.0 editor, but there's currently no plan to add this to the v1 editor.
It can sound painful to have to make back & forths betweeen UE4 and the popcorn editor to see how the effect actually looks like when tweaking it, but in practise it shouldn't be that bad, the UE4 plugin can quickly hot-reimport the asset so you can have the two running side-by-side. Agreed, that's not ideal, that's one of the reasons we made all shaders customizable in the upcoming v2.0 :)
If you want to discuss this more in depth, we might be able to work something out depending on your project's needs. You can send us a mail at support at popcornfx dot com.