I downloaded your blend file and reviewed what you are doing but there is alot of the project missing so I can only answer you based on what you provided.
Although you can animate color the way you have in Blender it is not appropriate for Verge3D.
Given you are just changing RGB values you could easily modify the shader and control the animation in Verge 3D and not have to bake or use any maps.
Remove the keyframes you created in the color palette of the emission and transmission shader. Attach a combine xyz node to transparent and emission nodes and then create value nodes as inputs to the xyz node. With this you can then either:
1. Assign values and keyframe the values and then use the play animation puzzle
or
2. Assign and control the values in V3D via puzzles to achieve the animation you need.
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