I have a couple of comments: Firstly, you probably need to employ the services of a lawyer. There are some tricky legal questions to answer.
I own a Lot within a scheme in Queensland which was built 60 years ago. My Lot configuration in the bathroom differs slightly in configuration from the original plans. This is not unusual. Changes to the building plans often occur during construction. The finished complex or unit may not be the same as in the original plan. This is by no means illegal.
If a purchaser buys off the plan then the owner often exercises their right to change some elements at the build stage. This may have happened in the bathroom at your Lot – particularly if changes to placement of plumbing fixtures occurred. Its always cheaper to make changes at the build stage. Maybe the original builder offered an upgrade such as a spa bath?
A changed plan does not necessarily mean that the responsibility for the waterproofing falls on you. If the bathroom was configured differently at the initial build stage then the water proofing should still be the responsibility of your strata scheme.
Having a bathroom that is different from other bathrooms does nor prove definitively that the bathroom was changed after it was built, nor does it prove that it was illegal.
Incidentally, glazing, waterproofing, termite barriers and pest treatments are elements that are covered by certification issued by the manufacturer or installer.
A Final Occupation Certificate is issued to an owner on completion of building work. It certifies that the work complies with Council conditions of approval and the Building Code of Australia. It permits the house to be occupied. However, the Council Certificate is limited in scope – it does not certify absence of defects.
I am not a builder or a lawyer but I believe that your strata scheme is wrong to blame you for this problem without them first establishing when your bathroom was constructed (e.g. during the initial construction, or post construction), and when it was certified and whether it has been properly certified.
If the owner’s corp can PROVE that your bathroom was modified after the building was constructed and had passed its original certification then you may have a bigger problem. The buyer beware doctrine generally applies.
The only recourse buyers have against a former owner (and selling agent) is an action in damages for misleading or deceptive misrepresentations about the structural soundness relied upon by the buyer.
Taking this action in court is a very difficult, costly and stressful path to take. Unfortunately, sellers do not necessarily have to disclose defects of which they are aware.
For now though, if I was you I would get a plumber to fix the shower with the silicone to stop it from leaking, and wait until the owner’s corp provides proof that you are in the wrong. In my opinion, they have not done this yet.
Keep the plumbing receipt! Adjudicators generally prefer repairs to be undertaken by competent tradespeople.