Could use OVR Toolkit to program the FMS in VR, but probably harder (never tried it).
It's actually easy enough to program the FMS in VR as I have my navigational stuff on a different PC, so just lift the headset to get whatever codes I needed. But it is a little easier doing the main bit in flat screen (slightly less wobbly) then entering VR mode - which is a very nice feature! Once the route is in, I don't need to come out of the cockpit again as I can see my routes and altitudes and such in the FMS.
It might be nice to have access to some info in the cockpit. If I remember a previous version of MSFS had a knee board or something, would be nice to be able to jot down notes, or in the case of VR be able to import a PDF or something with info that we might find useful.