Woot, finally some more rubble clues! Well at least one clue. Here's what Stormwaltz had to say on the Sage Tower:
The spawn of rubble is not dependent on any quest's state, nor is it admin triggered.
Short and to the point, but goes a long way toward helping us figure it out. So if it isn't related to the state of the Queen quest and if it isn't triggered by an Admin, we need to examine other elements to see what might trigger it. Could the answer lie in the East Fork Dam? Or some other dungeon? Maybe this is the clue we need to finally figure this out!