Vanilla Minecraft has extremely limited automation. One big issue is that command blocks cannot affect other command blocks. Something like a simple counter that isn't hardcoded is extremely difficult/impossible. You can build counters with redstone circuits, but getting the result into a command block is not possible AFAIK.
Plus, command blocks are cheating already. There are a number of mods that could have made this much easier/faster/more elegant/buildable without going into creative mode.
The design in the video takes a fairly simple concept and basically copies it for every single voxel in the build area, which is why it has such a crazy amount of duplication. It's spooling out each chest into a huge line, and then doing a quick compare to see what kind of block is in each spot and feeding that to the command block. The framerate suffers because vanilla hoppers are horribly coded.