Only with the NXi, the VFR map, and the PMS GTN 750 in WTT mode. As a workaround, if you’re using those units and fly mostly in the US, you can uninstall Navigraph data temporarily, as the sim uses the exact FAA data already. For other regions you may have to weigh the pros and cons.
The issue will only surface when attempting to input waypoints directly in the units in question; if you load the flight plan from the world map or load a PLN file into the world map, your waypoints will be transferred to the NXi.