From your in-depth description of the colouring process I could whip up a workflow in TVPaint as easy as this. All the elements are there, you just need to know how to use the program. Keywords: preserve transparency and colour lines, automatically fill display/above, and of course use different layers. Believe me, it's not the software doing the trick, since we did self-ink lines and shadows and all that stuff on paper/cel in the 90's without any problem. And that was the time when you had to do separate passes under the camera for a shadow or a highlight!
BasementProductions:
You're the first person I know who preferred the Blender interface to AS. I have the opposite experience, AS running on everything including my toaster, and being simple enough my 82 yr old father could use it.I tried AS once and didn't like it, mainly because of the interface. It was very cluttered with features and was too heavy for my machine