What sort of pipe? What is the neutral load? Any chance you could change over to an isolated phase installation? (3 pipes for phase A, 3 for phase B, 3 for C, 1 for N)?
The reason for section 310.4 is to ensure equal division of the current amongst all of the individual wires that are paralleled to make up a 'single' conductor. A problem with section 310.4 is that there is no specification for allowed tolerance or deviation. For example all conductors are required to be the same length...but no two length measurements are ever _exactly_ parallel, and 310.4 doesn't provide any guidance on maximum tolerance.
Heck, 2 conductors of the same nominal KCMIL will have different actual cross section due to manufacturing variation.
My gut tells me that current distribution differences caused by mixing THWN-2 conductors with THW conductors will be smaller than those caused by the nature of being in different locations in the duct bank (magnetic or thermal gradient effects). I have not done any sort of engineering calculation to verify this gut feeling.
There will be a difference in the impedance of the conductors with the different insulation systems, because the dielectric constant for nylon is different from that of PVC. But I am betting that this difference will be small, and dominated by the resistance and inductance of the conductors themselves.
-Jon