Just self-reproduction is a different problem than breaking down X energy source and moreover, the breakdown of each given source of chemical energy is a different and hard problem (the breakdown of cellulose by bacteria took a long time to evolve, for example). So creating a "breaks down anything" micro-organism (or nanite or whatever) merely by doing a bit of haphazard DNA manipulation doesn't seem like a big danger.
If you had human who grasped the broader principles behind micro-engineering and wanted gray-goo, well, then you'd have reason to worry. There's little evidence of this, however.