Re: moving a 5 frame nuc into a Warre
I think your plan will work for moving the bees into a Warré.
But after that, it will be more difficult to get the bees to move into boxes placed on top. Unless there is a strong flow it is hard to get the bees to move into a box placed on top, because it does not have combs or comb foundation. I suspect that is why Ēmile recommends adding the supers underneath, it's easier for them to slowly expand into.
As an aside though, I have heard of Warré beekeepers adding supers on top during strong flows, to get more honey. That's because if they waited for the bees to move the brood nest downwards it would take too long and the bees stop collecting honey as they have no where to put it.
"Thinking Inside The Box"