Disclaimer: this is as theoretical as racing in Mexico...
From the OBD2 test perspective, the Readiness Monitors can be set Ready, Not Ready or Unavailable. Not all cars have all monitors available, so the test can only look at the ones that are. The S197s have quite a few, and the Spanish Oak ECU is a pain to deal with.
Generally, once you flash the car with a new revision of the software, all available Readiness Monitors go Not Ready. Going through the OBD2 drivecycle the monitors should then go Ready. If a condition is present that warrants a fault, once the applicable monitor is Ready, the code will be triggered in either pending or current status depending on the fault type. Most OBD2 tests will allow one Readiness Monitor to be Not Ready, but not more.
Now, if the tuner turns off the rear O2s, the corresponding Readiness Monitor will basically sit there in Not Ready. The rear O2s are not sending any faulty values, they're just not sending anything at all. From a software perspective, the rear O2s either need to be switched back on, or the Readiness Monitor trying to set Ready need to be set Unavailable. To further compound the issue, some Readiness Monitors depend on each other to set. This means that there may be more than one Readiness Monitor that has to be set Unavailable, or the car will fail since they will sit in Not Ready.
Some people go the hardware route with non-foulers, MIL-eliminators, and so on, where others go the software route through the tune.