I just realised I can bake to unity's default standards after watching this video which means I can use standard shaders.
This will save a massive amount of time!
Ok so I've tried using the standard shaders on a baked character but I'm getting some strange behaviour.
I've baked a lightmap for the goblin using sprite dlight..
But the results I'm getting are strange..
The point light is to the right so the lighting on the shield is correct (although it refuses to light from the top and bottom (only from left or right).
Despite the head being the same orientation in the atlas, it will only light from the left when the point light is on the bottom left.
On the body top and bottom lighting are reversed and side to side lighting doesn't work at all.
The left and right lighting works on the fist but the upper arm seems to have reversed lighting also.
Honestly, I'm at a loss here.
When the image is flipped (negative x scale), the same problems remain.
I did a test on the individual parts and normal mapping just to rule out any problems there (they share the exact same material as the goblin character).
As you can see with a point light on the X they are lighting correctly (even when rotated), but the goblin below still has erratic lighting.
Here's an example where I've rotated the planes to show the lighting remains correct.
So the problem with flipped/rotated normals seems to be the way in which spine rotates the objects.
As for the problem with normals only lighting on 1 axis I'm at a loss..