Mentioned by Joe Rose.
Using AxMap1.CursorMode = tkCursorMode.cmEraseByPolygon you can erases parts of shapes of a single vector that intersects with interactive drawn polygon: (tkCursorMode API)
The vertices with the round circles are unexpected and I believe unwanted.
This is the result that I would expect:
I looked at the code and for this operation GEOSifference is used, that's why the result is what it is.
I think now that this behavior is correct and that we need an additional operation that is just removing the vertices that are inside the drawn polygon.
I'm closing this issue and will make a new feature request.