The advantage of performing superoptimization on IR level is that you have explicit data dependencies (due to SSA form). Thus you don't have unrelated instructions in between. Figure 1 of the cited Optgen paper http://pp.info.uni-karlsruhe.de/uploads/publikationen/buchwa... shows an example that can be optimized with IR-based superoptimization but not with a machine-specific one.

In summary, no approache subsumes the other one. Thus, it is worthwhile to have them both.