Recently, I was working alongside an HVAC guy, and I saw an interesting practice. To make a duct, he simply sheathed the open face of a rafter bay with sheet metal, and sealed the edges. This way, the subfloor above, and the two rafters, formed three sides of the duct.
I believe that this is what the code writers had in mind whan the exception was written into the code- as opposed to, say, someone actually punching holes in a metal duct in order to run their wires.
In other words, I suspect the exception is there for the convenience of the HVAC guy, rather than the electrician- though it also recognises that such a duct would be impossible to "go around."