I don't think SE regard the MSQ itself as content, but rather the precursor to content that provides the story setup for it. All their content is normally instanced - such as dungeons, trials, raids, etc. So if they were to have a puzzle involving pipes, they would probably put it as an actual mechanic in a boss fight.
They have done little bits of innovation with it, but it tends to be things such as NPCs following you, or you following them, aiming at something, the sort of features that were common in old single player games.
I think that has to be it. The team is there and some of these things are blatantly obvious, but they haven't done anything about them for 10 years. The only explanation has to be that they can't do it without permission, and either they don't request permission or the permission is not granted.it feels like they don't have the green light to be more creative
On top of that, an otherwise simple task most likely has to be put through numerous different departments to handle each segment of the task - when a single person could just do it. Chat bubbles has got to be an example of an otherwise simple feature that already exists for NPCs and just needed a minor code adjustment, taking years to go through all their procedures and polish.