Greg,
If the EMT is inside, you can ask the EC for a UL listing for approved use of the RX inside of EMT.
358.22 specifically allows cable to be installed within EMT.
Personally, as an electrical inspector, I would cite 300.3(B) as the code section to disallow this installation. I would argue all the conductors of the circuit were not installed in the same cable assembly; either all THHN [single conductors] are in the same raceway, or all conductors are in the same cable assembly. That is the code section I woulde cite in the correction notice I would write.
You can argue all you want, I wouldn't permit this installation and my boss would back me up.
