Just to be clear, there is no IFF.ini file. For each mission, you have a MissionName.iff file that decides what are the codes used by AI and what are the defaults in the DTC.
The IFF tab only affects your DTC, aka what will be the codes initialized in your jet when the DTC is loaded.
The mask can be any value from 0 to 32677(I need to add that to the doc). The influence on the generated codes is not straightforward to predict but it will have an avalanche effect : if you tweak it by one, it will drastically change all the codes.
You can do the civil airliner scenario if you set it to another team, without mode rotation for mode 3, and the TE creator just check what is the m3 code of the pseudo airliner to the guys flying.