I'm having trouble seeing what the actual technical downside to the install in the OP would be. We can take as our baseline "worst acceptable imbalance" the isophase installation allowed under 300.3(B)(1) Exception. So if we had (3) 3" conduits in a row, we could install 3xA in the first, 3xB in the second, and 3xC in the third.
Now delete the third conduit and move the C conductors into the A and B conduits. This is going to decrease the mean distance between conductors of different phases, and is therefore an arrangement that seems to me closer to having all the conductors in a single conduit. Doesn't that mean that the imbalance in impedances will be less than in the isophase baseline case?
If someone with more physics that me can point me to the relevant equations for capacitance and inductance per unit length for parallel conductors at a distance d from each other, I'm happy to do the math comparing the various spatial arrangements.
Cheers, Wayne