Personally, I would use those boxes as top feeder boxes and make more, but I am not experienced enough to know what the bees will do with that big of a gap. If they do fill it, those boxes might be hard to get off and stick down tight as soon as you put it back on.
I also would think, is it 2 deeps that have the gaps between them? If so pick the configuration that has the smallest between the two and put the biggest gap at the bottom between it and the bottom board, because most likely, you wont have to pick the bottom box up, pretty much ever, if you don't want. And they can fill it and leave it filled. And you can always change the boxes out anytime if you don't like it, so, it really don't matter. People use scraps that float to shore, so I'm sure you'll be O.K.