My view is that even with an engineering certificate, there is still a general power for the police to issue a defect notice for certain things that breach vehicle standards/ ADR's;
Examples would include: Atmo BOV's, excessively loud exhausts, Pod filters, turbo bell-mouths, window tinting, ground clearance etc.
Basically, I think people should err on the side of caution if they are relying on an engineering certificate is a cover-all that will prevent defects. It will definitely help but may not always fix the problem.
Just my $0.02