1. Because the rules prohibit a second entry of Europe unless transiting to another continent w/o stopover to/from NBO, ACC, EBB, DAR OR LOS.

2. You're confusing QF codeshares on AS metal with OW metal. If you want to go YVR-SFO-YVR that's okay (provided it's during QF's seasonal service on that route.) No non-OW metal allowed on these fares. You can use (unallocated it appears) additional coupons to go SFO-LAX-SFO to complete the west coast portion, again provided it's during QF's YVR period.

3. So this is a first class ticket? Anyway, HKG-JNB has F for part of the year.

Edited to add - Viajero beat me to it.