Albedo or diffuse map should not be combined with ambient occlusion map as it makes the result look muddy.
Yes. But that's common practice at the moment. Ambient occlusion is for ambient light, meaning non-directional. Like light from a nebula. The diffuse map shouldn't contain ambient occlusion, as that reduces the quality of direct light computations. (sunlight)
The only case where nebula light is directional is when you are close to some big object, which blocks the light.
If the move to adding support for seperate ambient oclusion maps in the engine is somwhere in the future, modelers should at least keep the maps seperated somewhere on their hard drives, so they can be added later. Or the mvp team can store them somwhere.
The other thing is that, for artistic reasons, a lot of modelers propably want ambient oclusion on their ships even for missions which don't take place in a nebula.
Something else: Why don't we have specular power maps?
Isn't that only when you apply the AO bake to the shinemap?
Why should anyone add ambient occlusion to the shinemap?