It makes sense to me...

For example if the the e-bike rider had to spend 1/5 of the energy of the unpowered cyclist (numbers chosen for the example's sake) that would be 1.1Wh/km they exert.

The remaining 12.9Wh/km would be what was discharged from the battery while riding (from using pedal assist and/or throttle features). This can be measured when you charge it back up at the end of the trip to the previous level.