As far as I know it is standard practice at many airlines to allow departments in the country where the original ticket was purchased to react to customer question/complaints.
Not efficient, I agree.

Regarding the check-in, doesn't this flight depart just after 23:30?
If you arrive more than 8 hours earlier surely that is not the airlines' fault?
Try checking in on SA from CDG. Their counters open 3 hours prior to departure!

I travel this route quite extensively and know that there is a thorough passport check in JNB due to all the people with fake documents etc.
According to my knowledge this is done by a separate company (a subsidiary of Swissport)
If you are checked in at another airport, the first carrier is responsible for your possible fraudulent documents, not KLM.

My solution: I checkin online and my printed boarding pass is waiting for me at the passport check, at the Business class side. Even for non-Elites.
Good service as far as I'm concerned!