That's pretty much what we do.
It is perhaps important to mention for someone trying to understand the vertical configuration, that when stacked on top of each other, the two colonies are are separated by a division board. (A hive mat with a notch out of one side)
So a vertical split, from the bottom up, looks like this:
First brood box with queen, excluder, super, division board (opening to the back), next brood box containing either new queen or cell (or eggs for that matter), excluder, super, hive mat, roof.
The foragers from the top box exit through the rear opening in the division board and go back to the bottom brood box.
The new queen builds up the top 'colony' while the bottom one carries on as normal. This reduces the swarm impulse. Once the flow starts, only the best queen is kept and the two colonies are reunited using newspaper. You end up with a big strong hive ready for the main flow.
If you end up with two really good queens, one can be used to start another nuc or to requeen another poor hive.
The downside is that if the bottom colony is pumping, then you need to lift all those top layers off in order to add another super above the bottom colony.
