There should not be a problem with supers (other boxes) on top. That would have to do more with the depth of the frame rests. With that spacing proper, everything above the deep is ok.
Use standard frames, and using the 9-1/2 boxes, just use the deeper side of the bottom board. More than enough room the compensate this small amount. I always leave the deeper side of the bottom board in use and totally ignore the shallower (winter) side.
If your going to stack these smaller hive bodies together instead of using them at the bottom, than make sure the hive boxes use the same number of frames. They will work up between the frames as long as they match up. If your going from a 10 frame box to a nine frame box and this space is not proper, than this will inhibit the bees ability.
Note...I almost have to shave a 1/8 to 1/4 amount off most boxes that I have bought. Seems that there is always way to much room after putting the frames in. I can buy boxes and frames from one source and sure enough burr comb will be between every box. Pumpkinpiper...I'd make the boxes, and after measuring with the frames in, you'll be surprised how close you are to correct sizing.