To get results for a particular layer, you will need to use "Layerp26" command in Post26. Then you can use ESOL (and ANSOL) to get results for a particular layer.
Yes, the warning is important. Post26 does not do coordinate transformations. The ANSOL documentaiton gives the below note: Shell elements: The default shell element coordinate system is based on node ordering. For shell elements the adjacent elements could have a different RSYS,SOLU, making the resultant averaged data inconsistent. A message to this effect is issued when ANSOL is used in models containing shell elements. Ensure that consistent coordinate systems are active for all associated elements used by the ANSOL command.