Yes the altitude compensation remains in the ecu as it is. Just looked today the formula for nitrous control module.
With TPS map you tune the basmap then you multiply the results with various compensations, most important being altitude compensation using suzuki stock methods.
Oxygen sensor works just fine, and you can even use the stock sensor to tune the cruising area for your bike - i.e. the IAP map. Just hook up a laptop and have a ride to see whats your AFR.
Basemap is stock map, even started my gen2 1441cc without problems.
Ignition maps get using group3 when you start using those. After that you need to press c to copy, ie.. unify the maps. I need to change that to unify to have same as gen1.
Good questions. Asking and then information sharing helps us all make the engines stronger and more reliable.
Hope this helps...