I've used these boxes with medium frames so I could move them into medium boxes. Any comb built on the bottom of the frames is easily cut off and reused if desired.
I also made some 4-frame medium boxes to sit on top so crowding isn't an issue.
As long as the area is filled with the resources needed by the bees to create the queen cell with, you should be fine. I've seen great producing queens come from a two frame deep split that was fed propperly and had plenty of pollen on the frames.
It's the density of bees that matters. A five frame nuc overflowing with bees will raise a fine queen. A five frame nuc that is sparsely populated will not.
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