Playing a goof around game, I discovered a couple of other areas where this isn't working. At the ACOK start, I won as Robb. I used neg_diplo to marry Dany and get a dragon. After waiting a long time for the raised vassal levies malus to run out, I declared a dragon conquest on Tyrion, Lord Paramount of the Westerlands. The megawar system did not trigger. I beat Tyrion rather easily. As soon as I gave him peace, I got a pop-up that I could imprison him for acting dishonorably towards me. I tried and failed and he revolted. This triggered the megawar system and the Riverlands became appropriately semi-independent. Since at the time I still had a large stack at Casterly Rock and a dragon there, the war didn't last long. It ended before I got the event to send ravens to vassals. The Riverlands did not rejoin the fold after the war. The system appears to be buggy with short wars.
That was a bit annoying, so I went back to a much earlier save and waited to declare dragon conquest on Tyrion again. Won easily again and this time did not choose to try to imprison him. I was going to wait a bit and do it when it would be a longer war. Never got to that as the Iron Throne declared a de jure war for the North on me. Again the megawar system triggered. Edmund Tully, the Riverland traitor, decided to join the war against me. Tyrion never answered the raven and never joined the war on either side. Instead he declared war on Edmund for a single province. After waging and winning a very long war, Edmund came back into the fold. Tyrion did not. He was not at war at that point. My only CBs against him were a few county claims. Going off what the above poster said, there might be a conflict because of the unique de jure status with the kingdoms in Westeros and the Iron Throne.
Finally, speaking of de jure status and the Iron Throne. I think this needs to be looked at. I was the King in the North. I won my independence from them only for them to try and get me back in the fold 10 years later. What do I get for winning that nearly 5 year war? 100 gold. Meh. Really, there is no reason for the Iron Throne not to declare a de jure war again in 10 years or when the next guy takes the throne. While it makes sense that the Iron Throne should try to reconquer territory, there shouldn't be a regular megawar over it and the Iron Throne failing should have some real consequences for them.