Hi Erik,
The separation of lines and fills as such wouldn't be difficult even without any extensions: you just duplicate the layer, go Edit Multiple Frames and for one layer choose None as the fill color and for the other None for the line color.
The trouble, as I see it, is the merging and breaking apart of the rig elements down to simple shapes. Often in rigs there are masks and other invisible elements used inside the symbols.
So, if such separation is to be attempted, one has to design the rigs in a very specific way; only use lines for the outlines and then when the rig animation is complete do the following:
1. Convert all animation to frame-by-frame
2. Merge layers (I believe that you can do this in Animate)
3. Break apart as many times as needed to get to raw shape level (the rigs should be designed with this in mind)
4. Duplicate this layer
5. Lock the bottom layer, activate Edit Multiple Frames, Select All and from the swatch palette choose None for the Fill
6. Lock the top layer, activate Edit Multiple Frames, Select All and from the swatch palette choose None for the Line
With this you should end up with having the lines above the fills on separate layers.
It's only 6 steps, and only needs to be done once when all animation is complete, so it's not that much manual work.
It should be possible to make it into a command. We'll think about it.
Hope this gives you some idea how you can approach the problem!