I build or adjust all of my equipment, full-size and nuc, so Top Bars are flush/even with the tops of the supers, and bee space is below the Bottom Bars. Or, sometimes I custom make my nucs with bee space above Top Bars (easier to add pollen sub patties) and below Bottom Bars. I usually only use a piece of plastic and a piece of 1/2" foamboard for nuc covers, but have begun making and trying a sort of "inner cover" consisting of a bee space rim of wood, covered by a sheet of masonite, beneath the foamboard covers. It was a trial I started this season, but they seem to work well, and I plan to make enough for all my nucs, in the future.
For my "production" hives, I use a combination slatted rack/screened bottom board, but in the winter I close it by setting the hives on a 1-1/2" thick piece of polystyrene foamboard - the same pieces of polystyrene I use on top of the hives in the summer. For my nucs, I use a 1-1/2" piece of polystyrene foamboard, with a 2" x 4" hole cut in it for ventilation, and the entire upper surface covered with #8 hardware cloth, to screen the hole and protect the foam from the bees. In the winter, I simply place a piece of plastic between the hardware cloth and foamboard, to reduce cold air infiltration. For my DCoates style plywood nucs, I make up cardboard with vent holes - those vent holes have #8 hardware cloth stapled over them, and the entire piece is saturated with either hot beeswax or hot paraffin wax, then stapled to the bottom. Sometimes, the odd colony, will even chew out the cardboard in a few weeks, but most do not bother it, and it's cheap to replace. Nuc supers are kept bottomless, or the foamboard/hardware cloth bottoms can be used with them, if you're in a hurry.
I do have a few nucs where I've attached a piece of hardware cloth over their entire bottoms, but this uses too much hardware cloth for my budget and still needs a piece of foamboard to reduce the ventilation in winter. And, one which has the entire bottom covered with hardware cloth, and then strips of plywood closing off all but about an inch wide channel down the center. It works well, but is definitely not as easy to work and clean as most of my other nucs.
I keep all my nucs on stands where they are thirty inches above the ground, at waist height. This makes them much easier to work with - very little bending or stooping. It also elevates them above where our Colorado River Toads can "clean them out" in a few nights. But the toads can still help keep the ground around the nucs, clean.