If the ecu can make automatic adjustments for air box mods why can't it for sports exhausts?

You raise an interesting point, self tuning is absolutely possible however the factory PCM does not implement it beyond basic ignition advance (to take advantage of higher octane fuel) and trimming the closed loop fuel based on O2 statistics. Some cars do run a wideband from the factory and can do a lot more but if you change too many things they will suspect a problem and throw an error code.

To answer your question they could if they wanted they however have specific emissions they must meet and hence they put tight tolerances on the O2 stats, if you change the exhaust you will change the exhaust flow, temperature and primarily the lag time for adjusting the fueling to adjust the mixture.

It will learn the new exhaust to an extent however the O2 performance will no longer pass the test as it will have learnt a new lag time that is drastically different from what it should be stock, this will raise a DTC as well.

The other issue is you change the load on the engine, this means you change the parts of the map that are accessed, these parts of the map may not be optimised for the conditions you are running causing excessive knock or too low timing resulting in worse performance.

Ultimately you need a retune to take advantage of increased timing/lean fuel and correct the O2 PID action.