If you want irace to see all 12 instances before removing any configuration, you can use "firstTest=12" in the scenario file. If you want that irace sees the 12 instances as a single block before any elimination test, then you should add also "eachTest=12". Of course, that would increase the computational effort since usually irace tries to remove configurations with less information.
However, the statement "I need to tune Algorithm X to benchmark Y" sounds like a conceptual error. Tuning for a specific benchmark does not show that an algorithm is good for anything but the specific problems in that benchmark. In fact, we know that there is an inflection point at which the more you tune for a benchmark, the worse your algorithm becomes for problems outside the benchmark. Reaching that point is easier with smaller benchmarks.
Best wishes,
Manuel.