A PCIIIr adjusts fuel depending on throttle position and RPM (it also allows timing adjustments but that was not your question). It does not have different maps for each gear, only for each throttle position and RPM. However, the PC works inline with the stock ECU, not in place of it, so in a sense the bike still has different maps for each gear but not because of the PC.
Maybe someone else can more technically explain this but the basis is that the PC allows you to modify the sensor signals, which changes the fuel/air ratio for any given TP/RPM. What I am not certain is whether or not the PC is technically before or after the ECU, but it is in the chain/circuit. That is why when you install the PC you unplug the stock ECU connectors and plug the PC connectors in line, making the PC part of the control circuit.
