I've never been asked to show my ID book at Or Tambo when I left and returned to SA. The PR Permit and port is good enough.
From what I've observed, it is not a standardized thing. Everyone I know seems to have a different treatment/experience when they travel. I have a friend who routinely gets scrutinized and interrogated and "threatened" with investigation of his PR/ID every so often upon return to SA from his travels( he insists this is because of prejudice towards his Nigerian nationality). He carries and produces his certificate, his verification document (he got his PR way back when the dpt was still issuing 2 documents) AND his green ID book. My brother travels with both as well (certificate and ID) but says that he was only requested to produce the certificate on two occasions/trips. The only thing he's been asked to produce is his ID and port since then. He travels rather frequently, for work in the immediate days after getting his PR, as well as for leisure more recently. Another friend whose mom and dad are longtime PRs says that they both always make sure they carry all documents, especially after a near-miss experience when mom was "detained" at immigration when traveling out of the country and nearly declared undesirable. Luckily, he was able to run to their home, grab the PR certificate, and race to OR to hand it over.
Another friend, who also has no idea why all these inconsistencies exist, suggests that once the official(s) at immigration the movement of the certificate twice (i.e. two round trips) and its authenticity, then the only required document is the green ID book and port thereafter. This only seems to be corroborated by my brother, though. Hence my never-ending confusion to this day.