In my humble opinion and from personal experience Waze has a tendency to keep with the original route as much as possible when adding a stop or deviating from a suggested route. Even to the extent that I was told by Waze to drive around and come back to the same intersection that my route deviated from. I've seen it happen when I've added a stop to my routes as well. It seems to me that Waze for some reason keeps the original route and calculates the shortest possible deviation from that original route. Instead it should recalcute the entire route with the new parameters. It would even be better to add the stops sequentially the way the route is calculated as with the Waze of today.
I know I'm not helping, merely trying to explain my findings.