JNB is not in Europe/Middle East, it is in Africa (albeit still TC2)
OP is thus trying to go
Asia-SWP-Asia-Africa-EME
This breaches the intercontinental departure rules and does not fall under the exceptions.
Routing it
ORD-HKG-DEL-HKG-SYD-HKG-LHR-JNB-CPT should be acceptable
(ie going to London via HK)
The US was acceptable due to the North American exceptions.
(e) Only one intercontinental departure and one intercontinental arrival permitted in each continent except as follows:
1. Two permitted in North America when one is a transfer without stopover.
2. Two permitted in Asia when one is a transfer without stopover or on direct single plane service between the Southwest Pacific and Europe.
3. For travel to/from or via Ghana, Nigeria, Kenya and Uganda two permitted in Europe when one is a transfer without stopover between Ghana/Nigeria/Kenya/Uganda and another continent.