Is over-watering the only reason for bark separation from wood stem during rooting process?
What else, when not over-watered, can cause bark rot in apparently healthy cutting?

Not sure the exact scientific reasons. 
But I think factors like too wet, poor air circulation, warm temps all contribute to rot. 
The pathogens are likely present even in the healthiest cuttings and it is a race between the cutting growing and getting strong enough to withstand the rot or getting eaten by the rot.
Pre-treating the cutting with an anti fungal may help but in the end you need to control the moisture, temp and air circulation to win.

Also it really helps to keep your newly recieved cuttings in fridge for two weeks. I got this tip from another forum member year or so ago. Its hard to do this though when you have your prised cuttings :)
And some varieties have special conditions to insure rooting others dont matter. I water root mostly but with sister Madeleine dark water rooting was failing and i switched to the 5 gallon bucket method and rooted very fast.