The comparisons I've seen have generally been comparing ROOT on a problem it was optimized for to HDF5 (or whatever) out of the box on the same problem. There

The comparisons I've seen have generally been comparing ROOT on a problem it was optimized for to HDF5 (or whatever) out of the box on the same problem. There are a half dozen knobs to turn in any of these libraries, if you don't turn them I'd be skeptical of any general conclusions.