I'm not sure if they would have to create a separate system to make the scenes unskippable. It's not just happening in the dungeon - it's also affected the version in the "Unending Journey" cutscene viewer. So whatever they've done, it seems to be a blanket change to that cutscene, however you access it, rather than a targeted "prevent skipping while in this dungeon" system. (And on a scene-by-scene basis as the post-final-boss cutscene in each dungeon is still able to be skipped.)
There's also already an option to turn on auto-scroll for other cutscenes, and there are other scenes that can't be skipped - like the "waiting to see if the door opens" scene in the Lost Canals. So both those systems exist in the game already.
I'm not a programmer, but I'm guessing it would be just something like a small change to disable the 'skip cutscene' button and automatically turn on auto-scroll for that file?
I think they chose to do it this way (rather than more complex adjustments or inventing a "sometimes enabled sometimes not" system) because it was a way they could change it without having to invest time and work into rebuilding how the system handles it.