If I remember correctly, the torque specs on this nut are misquoted in the manual
and are way too high (like 60 instead of 20 ft/lbs or something). It may be that the last time it was installed, the wrong value was used.
If you lock the back wheel with the bike in gear, that should keep the motor from turning but there is a lot of movement between the crank nut, through the transmission, and throughout the rear chain. It's best to lock the primary side, or at the pistons (if the top end is off).