They were rectified and then certified by other (manager) LAMEs. It seems that the FWA didn't consider the doors an airworthiness issue.
True, but this judgement seems to be that airworthiness is not the issue at hand. It seems to be more of a
"you didn't do explicitly what your employer told you to do and I find it suspicious (which you are guilty of) that you found these defects during a time of PIA for the sole purpose to create industrial pressure on your employer"
Justice John Logan found the regulation was not a "workplace law" under the Act and so was not a source of workplace rights.
From his point of view its 2 separate issues. He's made his judgement on workplace law not civil aviation law.
So taking the whole sunstate issue out of this judgement,
there is no workplace protection for you if your employer coerces you to certify for an aircraft that is unfit to fly under threat of being stood down or sacked.
The CAA regs you work under offer no workplace protection. Basically, you f*** up you get strung up by CASA. You don't do what your boss says you get strung up by FWA. There is no legal middle ground or one overriding the other if those 2 laws conflict - in a possible situation where the LAME refuses to certify for a defect he in good faith won't do and the employer compels him to do.