Just like you can apply a custom transformation to an EIB created using a custom report, you can apply one to an EIB created using a Workday Web Service. The steps to apply the xls document are the same. There is an example on Workday Community that is specific to the Get_Workers Web Service Operation called "Extracting HR-XML Using GetWorkers & EIB". You may wish to follow this example and compare the output of the file with and without the custom transformation.