The OC is obliged by law to charge everyone for work done on common property, the costs shared according to their unit entitlements. However, if you feel the work on your balcony in not necessary, and you are being unfairly impacted, you can apply to Fair Trading and NCAT for orders that the work not be done. The cost saving to you will be minimal, but you will be spared the disruption and loss of space and amenity. Have a look at section 232 and consider raising the issue through mediation at Fair Trading, in the first instance.
Regarding the legal fees, if you do go to NCAT and the OC loses, then the cost of their legal action against you must be raised from a special levy from which you must be excluded. That said, you have to take it to NCAT and you have to win.
I would forget the issue of the $3000 limit. It would cost you more to argue that in the Tribunal or a court than you would save.
Going back to your original post, you say the OC’s lawyer: “has advised us we will need to take on all liabilities for the balustrades which includes future owners. We have advised we will not accept the bylaw and its liabilities.”
This is standard practice when one owner wants something done differently with common property attached to their lot. If you are sure your balustrade is building code compliant, why not go with this?