The Stock ECM in both a Car/Truck work the same as the HD ECM does. The TTS is just a tool that allows for the tuning to be changed within the ECM, it also comes with many tuning aids that all the other competitors have tried to make there own version of. The thing everyone needs to remember is the ECM is what is making all the decisions when your riding your bike. What you or I believe is right or wrong doesn't matter, it does what it feels is right, and for the record it always wins! Sound like anyone else in your life?.
The O2 sensor is just reading what it see's and passes that signal back to the ECM. If the signal is wrong due to exhaust leaks, poor placement in the exhaust or any other mechanical problem it doesn't care. The ECM then processes that signal based on what is programmed into it. It doesn't know if the signal is right or wrong. If the ECM is not told that it needs to correct the signal it will not do it. It believes what it is told.
This is the issue with the aftermarket O2 units, they do not measure and feed the necessary information to the control circuit to allow it to make the proper corrections and you end up with poor quality readings and the control doesn't know, so it just starts adjusting based on what it's told. So who's to blame here? It isn't an ECM issue, it isn't a Tuning tool issue, it IS a O2 kit issue and that is where it needs to be fixed if you plan to use them. There have been several articles over the years showing the issues and year after year nothing changes and they keep pushing them out the door just as they are. I've attached a copy of just one of the many articles on them being tested and it only shows a few of the issues. This was from back in 2008 - 2009 timeline if I remember correctly. It's sad to say they haven't gotten any better from the testing we have done.
If you have proper installed and working narrow band sensors and a proper tune running Closed loop there is no need for more than one tune to be installed in your bike. Get on it, ride it, and enjoy it!