Sincerely i don’t know any way for auto-baking multiple objects in a raw in blender.
If you take a look at my project ( Carcassonne Medieval city ), i bake each wall and each tower ( for light and dirtmap ) one apart another, and by hand. 
I got all control but each bake is quite long for giving this final result for the whole city:
The pic is downscaled and highly compressed and therefore crappy jpg…
I think you gotta work on one ( of the most complex ) bone till you got what you want. And then do the same for all other bones…
Mebe you could ask for ppl help in the python script forum. I’m sure that what you wanna do can be automated with script but i’m too shitty coder for helping you on this 
Hope it helps 