One thing that would be great would be to create the Color art in a layer separated from the line drawing layer. This would make it easy to make clippin masks of the color layer without the need to paint frame by frame each frame in a different drawing layer or separate all layers through nodes.
Based upon your words and if I am understanding you correctly, this is possible and has been for many versions in Harmony.
There are 4 layers available and two have the names Colour Art Layer and Line Art Layer.
Built into the structure there is greater freedom to handle the layers everyone"s own way but you can choose to manage them according to your desired scenario as described in your post.
No, the thing would be to use the Color layer as a clipping mask. If, suppose, you will create the color in the Underlay to paint the shadows in the Color layer, also would not take it as a mask. You should separate each layer individually through nodes when you could simply create the color in a different drawing layer and facilitate the clipping mask process.
Could the Layer-Selector node help you to do what you want?
It allows you to “filter out” the art layers you want to use. This module combined with cutter nodes might allow you to get what you want.