While this will perhaps result in somewhat artificially inflated scores, there may be no reason to think that it would benefit one system or approach more than another, and this concession might seem reasonable considering the fact that there is likely to be no completely foolproof way to perform alignments.
the potential harm that this behavior manifests in terms of the technology development process--which, to our knowledge, has never been brought to light--is that it creates a situation in which uncontroversially positive changes in system output may result in a dramatically worse score, and likewise negative changes may result in a dramatically better score.