Gengoguro's seal in the Tale of Gracefulness was placed by the Purple Pupil. As for why the Black Core Crystal under Shangri-La didn't explode, it was a complicated question. As far as I know, the energy of the Black Core Crystal is very powerful, but they are sealed deep under Shangri-La instead of exploding directly. This might be related to the composition of the Black Core Crystal and its energy source, as well as some secrets and agreements between Gengorou and the Purple Pupil people. I can't go into the details, but it's a complicated mystery.