The copydcard command for use with overlap calculation is currently supported in FDE, varFDTD and FDTD. Therefore, there is really no straight forward way to save mode profile in EME into fld file/dcard and use it in overlap calculation.
It might be possible to use a workaround in order to create the dcard, but it will require some scripting.
A) You could try to save the mode profile data from EME into a mat file in a rectilinear dataset format that can be used by import source in FDTD. Afterwards, you could use the FDTD import source in a free space and a frequency monitor to record the field profile. This frequency monitor data could be then used for mode overlap calculation as it is shown in the short script example in your question.
The use of an import source and related datasets is described here.
The obvious drawback of this approach is that you need FDTD solutions
B) You could extract the E and H filed data from your EME mode profile similarly to option a, but then you could use a script to manually create the fld file that could be later used for overlap calculation in MODE or FDTD. I have attached an example script that creates fld file related to this example.
usr_create_fld_EandH.lsf (3.6 KB)