The vehicles engine sensors (air temp, engine temp,TPS, IAC, etc.) all provide information to the vehicles ECU that modify the fuel air ratio & ignition timing at the optimum ratios or timing to both provide the best power, fuel economy, and still maintain EPA compliance. So there is no way to say that the calibration makes the vehicle run richer or leaner or adds timing or takes it away, because these are consistently being monitored and changed based on the driving conditions and situations.
While all the sensors above and the O2 sensors surely play a role in fine tuning the fuel metering, but you can bet your ass there's an open loop base map based on TPS and rpm that are the primary setpoints used to meter fueling. That's why it makes little difference whether or not the O2 sensors are unplugged. I'd bet that the bike would run fine even if all the sensors except the TPS and tach were lost unless Vic just added something to kill the engine in such an event.
If the system were a true closed loop system, it would compute an output based on the inputs. If those inputs changed because of different system conditions i.e. better flowing peripherals, the calculations would take that into account. There would be no reason to reflash the ECU if that were the case. But since it is actually running primarily on an open loop map designed for a specific set of stock peripherals, the ECU must be reflashed to update said open loop map for the freer flowing peripherals.
A Stage 1 map may well run at or near the same base a/f ratios as a stock map. But it would be doing so when operating the machine with freer flowing peripherals. That means it would run richer than stock if you downloaded Stage 1 software in a bike running stock peripherals.
Even a PC-V has a set of fuel metering values that it defaults to if it were to lose an O2 sensor. The sensors it uses are wide band not the on-off cheapies that come stock on our bikes. When the sensors are connected, those really are running a closed loop calculation.
Imagine a closed loop control as a game of higher or lower. Say you want to meter fuel to obtain an a/f ratio of 13.5. Say it's first guess results in metering enough fuel that it runs at 12.5. The wide band sensor would report that value and it would try again and maybe get 14. Again the wide band sensor would report that output until it finally honed in on the proper amount of fueling at a given TPS and rpm setting.
Our narrowband sensors can't play high low. They either turn on when the value is above stoich or turn off when below. They are simply there to try and keep the fuel metering above stoich while its idling or cruising. They are ignored during hard acceleration.