How does Li and Durbin's BWA paper compare alignment programs on real data?
What they are pairing is the RNAseq data with the reference genome: as the legend of the table 2 says:


  The 12.2 million read pairs were mapped to the human genome


These softwares align the same read to the same genome. They aren't comparing if it is mapped to the same location, only how many mismatches has each program.