There are two reasons to have a waypoint: 1. you want to stop there (for instance having lunch, there is a cheap petrol station), 2. you want to pass there (change a calculated route for some reason, you like the landscape better).
There is a basic difference between the reasons. One side is #1 and #2 is the other side. For #1 you want to be warned, but may be not for #2.
So besides of choosing to include a waypoint on the route, there must also be a choice between #1 and #2. A solution could be a radiobutton-type choice that when a waypoint is activated you can select "stop" or "via"; "stop" for #1, "via" for #2. If you have chosen for an active waypoint and "stop" you could get an announcement else not.
There can be an error present when you revers a route in the "routing points" screen. When you have a waypoint as via on a highway the point is NOT moved to the opposite lane(!). (Version 3.0.125) .