In order to support drag-painting blocks you need to set the GUIUtility.hotcontrol property while painting (See https://docs.unity3d.com/ScriptReference/GUIUtility-hotControl.html).

The Prefab Mode checks if the hotcontrol is set and delays autosaving until it is released again.

Example for your editor script:

private void OnSceneGUI()
{
int controlID = GUIUtility.GetControlID(FocusType.Passive);

if (GUIUtility.hotControl == 0 && Event.current.type == EventType.MouseDown && Event.current.button == 0)
{
GUIUtility.hotControl = controlID;
Debug.Log("Grab hotcontrol");
}

if (GUIUtility.hotControl == controlID && Event.current.type == EventType.MouseUp && Event.current.button == 0)
{
GUIUtility.hotControl = 0;
Debug.Log("Release hotcontrol");
}

.....