I believe the code says they aren't allowed in the same enclosure. I wouldn't normally consider a manhole to be an enclosure.
I assume the the wires open inside the manhole?
For 208 or 480V, it seems like you should be able to put a pull box or something else inside the manhole to separate the emergency power from the normal power. Then it wouldn't be much different than haveing both in the same room.
For higher voltages, it might be another story.
It seems like you should ask the AHJ what he/she thinks.