If you count on the MRA "avoid highway" option (or any other option for that matter) then it can go wrong because a GPS device with different settings can still interprete the resulting GPX file completely different.
In my humble opinion, the best way to make a route is to put sufficient waypoints on the whole route and that can include putting some waypoints on a highway. The options in the routeplanner toolbox do not influence the settings of a GPS device.