The idea is to compare the two systems given the same type of input: if the reordered system learned a better phrase table, then it might outperform the baseline system on un-reordered inputs despite the mismatch; on the other hand, if the baseline system learned a better phrase table, then it might outperform the reordered system on reordered inputs despite the mismatch.
the results in Table 6 did not settle our question: the reordered system performed worse than the baseline on unreordered data, while the baseline system performed worse than the reordered system on reordered data, both of which can be explained by the mismatched conditions between training and testing.