I've filled out those Application to Modify forms many times when it came to my CA18DET 1600 and SR20 supercharged 200B. Its a form where you basically state what modifications you have or intend to have. Lodge it, and you'll be sent a list of requirements for any engineer to certify. I know when I did the CA18DET conversion they requested a chassis strength test, brake upgrade balance test etc. Cost me like $1000 to get the Engineer to certify all that. I remember it was a nightmare getting approval for my adjustable radius rods and control arms, roll cage, and massive 330mm brake upgrade on the 1600, then there was the top-mount VG30BB.
When I did my SR20 supercharged conversion to the 200B, I didn't need the chassis strength test for whatever reason. But it had to have a Regency inspection for brake upgrade, wiring etc ... without needing an Engineers report. The inspectors were doubtful, but they passed it. Mostly because I filled the forms required and I was trying to do the right thing.
I've never been questioned on those cars ...
However I did get another 200B defected before that. Had a L20B punched out to 2.2 litres, big cams, twin webbers, big brakes etc. Had an Engineers report, but the two bike cops wanted to defect me anyway. They couldn't touch a thing on the list, so they did me for tyres (80% at the time btw) which was rubbish, and put me down for a Regency inspection. Drove straight to the cop shop, showed them my eng cert and the rubbish defect. They promptly removed it immediately without charge. I had the right documentation to go with my car, and they had no right to defect it.
The short answer is: if you have submitted an application to modify and have the mods approved/certified, then the cops should be satisfied with what is on the list.