I was surprised by the work on the ura too, however, the Nakayama Shouhonyama + Mikawa nagura combination is very fine so I guess there's no worry about flattening on that side. I use the same Shapton diamond lapping plate that is in the video, and it is surprising how these Lvl 5+ Jnat finishing stones wear with use and need frequent flattening. I found his admonition to keep stones flat an interesting part of the video.
Deburring on a loaded strop is definitely a knife sharpening thing. I don't think I've seen it done on a kamisori before but it makes sense.