My team is working on a fighting game. We usually make the humanoid animations in Maya and import it into Unity. These animations only contain bone movement and nothing else. We would like to create separate in-Unity animation clips that run synchronized with the original humanoid animations to tweak engine components like hitboxes in sync with movement. The imported animations cannot have additional curves added to them outside of the ones that tweak animator parameters, which both has a horrible UI and also make it difficult to manage when we have upwards of 20-100 hitboxes per character.

Someone mentioned Mecanim's sync layers, which definitely help. Now we just need corresponding animation clips for each state. The problem then is that the animation window, to my knowledge, at least, does not allow you to layer multiple animations (i.e. seek the humanoid animation while editing the hitbox animation), which presents a particular problem in workflow.

Is there a good solution to this kind of issue? This doesn't seem to be an uncommon issue to deal with as Unity game devs.