That statement should not increment Handler_commit. If you examine what is REALLY happening I think you will probably find that whatever you’re using to run that query is running a COMMIT right afterwards.
I’m not seeing the same behavior on 5.0, so this might be something that changed in 5.1, or in the plugin version of InnoDB. It could have to do with changes in the storage engine API. I’m not sure what to think about this. It ought to be a no-op anyway, but I’d like to understand this more.