Concerning differences in alignments between the two alignment types, exact vs. approximate, an illustrative example where the approximate model fails and the exact model does not is ('false' alignment based on the approximate model indicated): r ee n t e r e d r i E n t @' r d r i E n t @' r d which nicely captures the inability of the approximate model to account for correlations between the matched-up subsequences.
while the segmentations of the three shown sequences appear acceptable, a matching of graphemic t with phonemic n, etc., seems quite unlikely.