I do not believe the proposed action will do anything to reduce the harmonics. To get rid of harmonics requires frequency filters.
Questions that affect how the Wiring Rules apply is whose transformer it is, and whether or not it supplies any other installation.
Also where is the point of supply?
Assuming that the conductors from tx to swbd are "consumer mains"; then "3000" allows only two options.
The normal option is as per Fig 5.1; with the mains neutral being actually not just a neutral, but a PEN conductor.
Option 2 is illustrated in Fig 5.2; with no MEN link, MEC, or electrode within the installation, the mains N is just an N.
This option is only allowed under the Exceptions to particular clauses.
5.5.1.1; which allows for the electrode end of the installation's MEC to be connected to something other than an installation earth electrode .
5.3.5.1; which allows the installation MEN connection / link to be somewhere other than at the installation's MSB.
Those Exceptions cover 2 of the 3 components that make up the installations "main earthing system" (as defined in ESR 4).
The 3rd component is the electrode [5.3.6], and there's no Exception needed for that because the clause doesn't dictate the precise location of the installation's electrode.
While these Exceptions allow for several sub-options as regards the detail (eg exactly what the MEC gets connected to);
there are really only the two options; making it an "either / or" situation and you have to choose one or the other.
Therefore having both a full main earthing system within the installation (as per normal), and an additional earthing conductor back to the substation, would be non-compliant with Part 2.
In particular, it would, as you've noted, result in load current being carried in a protective earthing conductor; contrary to 8.3.8.1 (a) (also, in 2018 edition, 5.5.2.1).
Therefore, if the engineer insists, he will have to produce a certified design for work to Part 1; i.a.w ESRs 58 & 59.
Required documentation for Part 1 work is set out in 1.9.4.
Calling it a "bonding conductor" doesn't make it one. Equipotential bonding is about dealing with voltage difference between exposed conductive parts and extraneous conductive parts.
Touch voltages can be cased by the high fault currents carried by the protective earthing system; resulting in voltage along the length of the PEC.
This effect is mitigated by using one of the 3 methods of "fault protection" permitted by 2.4.1. In this case almost certainly using automatic disconnection of supply, with the mandated time limits for operation mitigating the risk of anyone receiving a shock from simultaneously accessible parts.
The other main case of touch voltage is differences on potential between parts connected to different buts of land. There are many causes, but these are what equipotential bonding is designed to deal with.
Harmonics cause a lot of problems, but not touch noted for producing touch voltage. Since that's not the problem being addressed, calling this proposed conductor 'bonding" is just playing with words.
You don't state what the symptoms are; but since there are large VFDs involved it's likely that there are induced HF currents (as distinct from "harmonics"), that may well be causing HF touch voltages. Clause 5.4.8 refers (though not in any detail).
This is another form of touch voltage, and as for EPR, the answer is ensuring that all simultaneously accessible conductive parts are at similar potential. Fact is that normal earthing, designed for 50 Hz fault currents, is often a high impedance to HF. Therefore to deal with HF induced touch voltage, we need an earth path that has low impedance to HF
And if this is the problem, then again the proposed additional earthing conductor between MSB & TX won't do anything to help.
First step would be to ensure that the advice in the code of practice for VFDs has been followed.
Power Drive Systems (PIB 49); published by Radio Spectrum Management:
https://www.rsm.govt.nz/about/publications/pibs/pib-49/
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With regard to the detail of where the MEC can be connected, you can choose either Exception to 5.5.1.1.
Exception 2 allows for connection to a "neutral" bar if so required by the distributor.
However using a combined N&E bar would be non-compliant, as 5.3.5.1 requires an "MEN link".
The Exceptions allow it to be at the sub, but you can't not have one.