The Fill tool is a simple but effective colouring tool.
At the moment, the only way I can think of to use it would be for the shading colour guideines to be on a separate layer and use Grow Selection to cover them, but not cover the black.
You’d do the final visible artwork in black:
Then copy that layer and put it underneath and add the shading colour guide lineart:
Then you’d add a layer for Fill colouring, under the final lineart and set the Grow Selection value to cover the colour guide lineart. For this, the black lineart should be a greater width that the colour guide lineart:
As you can see, you’d need to adapt your colour guide lineart to the characteristics and limitations of that method.
It would be difficult/impossible to retrofit that technique to an existing animation and would be something you’d need to do from the very start.
There’s nothing wrong with passing work between different applications, as long as you don’t lose information and as long as it’s not too complicated and confusing.