I would just say that splitting a hive may not always quench the urge to swarm. There are numerous factors, in addition to crowding, that play into swarming. Some of these factors are initiated weeks in advance of the queen actually laying eggs in swarm cells. This may have been a situation in which the queen had "intended" to lay eggs in swarm cells, and your split just didn't dissuade her from doing so. The hive had "intended" to swarm, and the queen-right half of the split continued with that plan.
The really curious part of this is why you ended up with both swarm cells and supersedure cells in what I presume was the queen-right split? This is not common. Perhaps the queen had laid eggs in queen cups before the split and you just didn't notice them? And when you couldn't find the queen it was because the she had failed just a day or so earlier? By chance you just put all the queen cups with eggs into the same split?
I saw a somewhat similar situation last year. There were started swarm cells in the hive, so I searched and searched for that queen to make a split, but never found her. I tried again a couple days later and found supersedure cells in addition to the swarm cells. My conclusion was that hive had initiated swarming but the queen failed just after laying in queen cups. Then the queen failed, and because they were queenless they started supersedure cells. I don't believe that the bees would be able to reason that making emergency queens was unnecessary since there were already some swarm cells started.
As a side note, in general I don't think it's good practice to let a colony with only 2-3 frames of brood raise queens. This also is also in contrast to the standard practice of using strong queen cell starters and builders to raise queens. We had very good conditions lately and these splits were probably strong enough to adequately feed a couple cells, so you'll probably end up with fine queens. This is just something for new beekeepers to keep in mind.
Joe