Potential energy is energy, so it's not quite correct that New Shepard had 0 joules at 100km. At 100km and 0 velocity it'll have about 1 gigajoule of energy per metric ton of mass.
I think the point was to illustrate the difference in energy requirements for the rocket to impart to the payload.
That said, re-reading Elon's article, he did explicitly say _kinetic_ energy in the 120GJ figure, in which case 0 is the right number for New Shepard at 100km.