The ECU will most certainly learn and try to adjust timing based on perceived knock events. It does this through the Dynamic Advance Multiplier (DAM.) If your tune isnt garbage then the ecu will be able to accomplish this. It is still imperative to address those issues as soon as they arise rather than just let the ECU handle it, but the ECU does indeed have some built in measure of self preservation. There are a couple posted logs right here within a few posts of this one that demonstate this.
I am stunned a supercharged honda's ECU would not even be able to compensate for bad gas.....sounds dangerous.