OP - you're over-thinking this whole trip.

Looking at the SA customs website , it seems clear to me that you will be bringing in medicine in 'sufficient quantities for three months for own personal treatment accompanied by a letter or certified prescription from a registered physician', which is expressly called out as excluded from needing declaration.

Therefore you don't need to declare them, and you don't need to fill in a travellers card, and you don't need to go through the red channel.

If you normally decant all your drugs into one pack, why is this any different? You have the same risk that law enforcement will challenge you as to what all the drugs are, but clearly you have decided that the downside of mixing drugs (time delay while each pill is checked for legality) is outweighed by upside in convenience.... South Africa is no different.

And don't sweat the laptop bag/handbag thing. I regularly take a stuffed laptop bag on as second personal item on JNB-DUR/CPT flights without issue.