You get the warnings because when a dynamic grid obstacle recalculates a part of the grid graph, it will also recalculate the penalty and reset it to what it would have been if the graph had just been scanned. Since the AlternativePath modifier modifies the penalties of the nodes it becomes a bit confused when another script is also changing it at the same time. This will not break anything pathfinding wise however, but the effect of the alternative path modifier will be removed in the region where a graph update happens.
That it crashes the pathfinding system is a bug however. It seems I used the Debug.LogWarning(message, object) overload which cannot be used from a separate thread. To fix this, open AlternativePath.cs:108 and change it to use the Debug.LogWarning(message) overload.
You can prevent the DynamicGridObstacle component from modifying the penalties by changing it to instead of calling
var guo = new GraphUpdateObject(bounds);
guo.resetPenaltyOnPhysics = false;