Last week I was trying to route directly to the stop first then the final destination. It would start off suggesting the green route except that it wanted me to turn right from the N2 into Lourens (a block before Victoria), over the river, left into Sargeant then right into Victoria. As there are no lights at N2 & Lourens turning right across traffic there is often slower than turning right from the N2 into Victoria. Experience has also shown that there can be quite a hold-up turning right into Victoria from Sargeant so I tend to ignore this unless there is no other turning traffic ahead of me as I approach Lourens.
As soon as I pass Lourens, ignoring the suggested turn, Waze recalculates and switches to the red route and the ETA increases by four or five minutes. Once I ignore this and turn right into Victoria it switches to the green route again.
Assuming perfect traffic flow the green route is definitely better but as I found the other morning there was a hold-up on Victoria that lost me five minutes, so on that day the red route might have been faster. However there is just as much chance of delays on Broadway leading to the Lord Charles intersection so there is really no way to know which route will be better on any given day.
As you say there is probably just not enough traffic data for Waze to be totally accurate with routing in the area.