You don't always fly exactly over the calculated ETOPS/EDTO positions. As such, you'd be zigzagging slightly off the airway / CFP route.
Eg. If your CFP is calculating a distance from an off route airport for an EEP, due to many mathematical factors, including the earth's shape, the EEP won't lie exactly on your track, but will be pretty close.
Hence you plug it in the box as a waypoint and put Waypoints on the ND so you can visually see EEP/ETP1 etc.