Version Esri.ArcGISRuntime 100.12. Tested both in dotnet core and dotnet framework.
GeometryEngine.Equals(new MapPoint(0,0,1),new MapPoint(0,0,2)) returns true.
I reproduced it in a blank project, so no prerequsited needed.
This is a known limitation in the geometry engine.
> GeometryEngine generally operates in two dimensions; operations do not account for z-values unless documented as such for a specific method (for example Project(Geometry, SpatialReference) will transform z-values in some cases).
If you're interested in a full, exact geometry comparison, including Z and M values, you can use Geometry.IsEqual(). Depending on your use case, you might also find Geometry.Equals() helpful, which allows you to specify a tolerance.