First, my opinion is that the inspector is correct as to the intent of the code.
IMO, the conductor in question is an Equipment Grounding Conductor, not a equipment bonding jumper. I base this on the definitions in Article 100. I realize there is some room for argument here, and a lawyer could probably persuade a jury that the installation meets the literal wording of the code. However, the inspector has the authority to interpret the meaning of the code.
Note that the conductor in question is not only providing a bond path, it is also providing the connection of the various equipment to ground (earth) by connection to the GEC.
A 30 foot long bonding jumper in a seperate conduit is stretching the intent of the code, at least in the inspectors opinion. And I agree with him. Plus there are some implications on increased impedance of a long fault path that isn't routed with the circuit conductors.
The simple solution is to bond the grounded conductor to the service trough/CT installation. Then no other EGC or EBC is needed. The grounded conductor serves as the fault path and the bonding means.
Now, some have spoken of this "parallel path for neutral current".
On the line side of the service, there is no restriction or prohibition against having parallel paths for the neutral current. In fact, 250.24(B) requires this "parallel path for neutral current" when we have multiple service discoonects with metal enclosures and raceways. And, 250.92(B) allows the grounded conductor to be used for bonding on the line side of the service disconnect. This again will certainly create parallel paths with the neutral.
The prohibitions against the "parallel path for neutral current" are on the load side of the service, not the line side.
And this brings up another point. So in the original installation, if we simply bond the grounded conductor to the CT/trough installation, do we have to remove that 1" PVC with the "bond" wire in it? No we don't. There is nothing prohibiting that extra wire as long as the proper grounding/bonding is accomplished by the grounded conductor.
Edit: So, to sum it up, yes, the original installation is a violation of 300.3(B). And the reference to 250.102(E) has that 6 foot limitation for outside the raceway.