Thank you very much for the sample graphs.
Re diagram 2: The BPMN layout algorithm does not support nested pools. As far as I know, pools have to be top-level in BPMN (i.e. diagram 2 is not a valid BPMN diagram). So, I would classify this as "invalid input".
Re diagram 3: Due to the inherent complexity of restricted layouts (the restrictions being the rows and columns of pools), BPMN layout does not support mixed diagrams very well. (By "mixed" I mean that you have nodes in pools as well as nodes that do not belong to any pools.) The algorithm handles such diagrams by adding an additional invisble column and assigning all free nodes to the first row in that fake column.