In my opinion, to assign a default projection file, you just have to assign it in solidworks.
To do this, take a MEP, save as, then select the dwg format, click on option, then in DXF/DWG export option, activate the projection file and choose the path to the desired file.
Batchconverter is just a program that gives a list of files to be processed with solidworks so it is the solidworks options that are used.