So I believe the way it works now is that you do have to use the EFB. The flightplan should already be loaded in the EFB on the route page though so you just have to go to the bottom of that page and click “File Flight Plan with ATC”.
Then in the ATC window you choose the option to Request Instrument Flight Plan. FYI in career mode this option should be available without needing to do the above step, because the career mission will already have the flightplan ready to go in the EFB.