There, too, it makes more sense for the music to just fade away after the Atris theme... so it goes in Academy background music, and continues that way into what triggers next (Handmaiden scene or the PC being next to hawk)... IMO
Every cutscene ingame works like that. Except for the .biks, but well, they were made .bik's (and have no soundtrack for their ingame version, those needed to be re-created)...