We leave all of the factory OBD safety systems in place with our software. Misfire detection is active in our cars and you will get a code for it if it occures often enough for the ECU to believe there might be a fault, this the same as the stock software. The ecu can also pull timing on its own to a certain degree when needed. It is a target based system which adapts itself within a set range during operation and as posted already each cylinder is monitored and controlled individually. The ecu also has a number of safe / limp mode triggers in place to keep the motor safe during operation.
OP im glad your car is back to 100%