After disconnecting the stock 02 sensors, the stock 07 system is open loop. No possibility to self adjust. Depending on TPS-RPM-MAP it will deliver fuel.
With a PC you change the amount of fuel at specific TPS-RPM values. YOU (your tuner) has to tell the pc how much more or how much less. That amount of difference will be used since that time. No self adjust to age, wear or what ever. Without 02 sensors the system will also not correct for its own 'tolerances'. I've heard that the stock delphi system has a - or + 5% tolerance.
You can get that same flat afr line without the pc by changing the settings in the stock ecu. This is called the VE. Volumetric Efficiency. You tell the system how much air is passing the engine. Together with some constants and the load on the engine, this Efficiency is used by the ecm to calculate the amount of fuel.
I don't see any problems caused by the closed loop system. Or it must be caused by a base calibration that is way off. But that would be the same with a pc, if a pc is way off, you will have a bad running engine also.
But fact is that the stock closed loop system can modify the fuel delivery a lot. Put a stock 07 on a dyno, change mufflers and airfilter and ride the bike in closed loop, the afr will be corrected! Although you are riding in closed loop most of the time (depending on riding style), unfortunately you are not riding in closed loop all the time, so you need to have a good calibration to start with.