There is another option which I do often when I see the big discrepancies in the LNM loaded plans. After I save the plan exported to MSFS then load it in the sim I immediately save it back to the save files and then pick that newly saved plan and put it into LNM. Then all the waypoints and approaches match up.
If I don’t want to do that I simply generate the plan in LNM and manually input the plan into the Avionics while on ground. It can be very cumbersome though depending on which plane and which avionics are in use.