I'm pretty sure after looking over the video that it's not a Training Mode glitch for two reasons: the increased SP gain and the hitstun. With the 800 damage j.B, he gets 5 SP for the hit. Even the max charged version only gives you less than 4 for the hit.
Then, you have this:
The 800 damage hit seems to have equal or possibly more hitstun. I tried to capture these as accurately as possible at 0.25x speed but they may be a bit off. Both the points aside, simply trying this in Versus mode would rule out a Training Mode glitch as well.
Your second idea has some merit though as it could be a specific place/way you have to hit to get it.
The only other thing I could think of is a just frame or small number of frames during the charge that makes the j.B do critical damage (800) and even more hit-stun.