That NEC article refers to running different voltage systems within the same conduit or cable. It does not apply to running different voltage system in different conduits within the same duct bank. This is allowed. It is permissible to run a 12 kV circuit in one conduit, a 480 V circuit in another conduit and a 24 V dc circuit in a third conduit within a common duct bank. The problem come when you enter a manhole or handhole, since the high voltage must be isolated from the lower voltages.
We generally split out separate manholes/handholes for the 15 kV (or any medium-voltage) cables. Then if you use 600 V insulation for all low-voltage cables, they can occupy the same space in a manhole/handhole. The other option is to provide a barrier of some type within the manhole to isolate the 12 kV from the lower voltages.
It's good practice to keep the 12 kV ducts segregated in one portion of the duct bank. We sometimes put two duct banks in a common trench to increase separation, but this is not required by the NEC, AFAIK.