The HD has a MAF sensor. The ECU has the ability to see how much airflow is coming into the engine because of that. It will try to add/subtract fuel if the calculations are incorrect, but only will do this depending on the programming. The HD ECU is not programmed to have a wide range of fuel curves. It is rather narrow. To compensate for the increased pressure of air, fuel must be added to have the computations done by the ecu to be the equal as stock. You need to calculate how much airflow is entering the engine to determine how much fuel is needed, and what the ECU range is to keep the ECU happy. On a turbo or s/c setup, both do not have much boost at idle; if any. At high rpm, it will be under boost, and if you made your calculations right, you should be able to run a turbo or s/c on that fuel curve range the ECU has. Air temperature is also critical as well. What you want to consider is the fuel curve the ECU is able to adjust to, both low end and high end. How far can the ECU ecu trim the fuel. Ideally, you would want the injector duty cycle at the low end at idle and the higher end at WOT.The stock ECU has absolutely NO IDEA that the engine has a turbocharger hanging of it...how would it? The way around the pressure level difference on a MAP sensed engine is to "clamp" the output voltage at its N/A max level. That is a voltage that needs to be tested and logged BEFORE the turbo is added. Then...once the FI system goes on..that feature is then performed.
Now...I put an asterix (*) beside the Input signals because I have to point out that it does alter one input....the first EGO sensor. If you alter the fuel curve that the ECU has output...and the EGO sensor is not relaying back to the ECU what the ECU "thinks" it should be getting back...it will try and compensate. And..as you rightly point out...it can't do that very well...and thus throws a CEL.
My engine for the turbo is not stock. It is completely custom with custom ground pistons that make the compression ratio where I want it. On the engine dyno (bench test), I have tested the stock pump and injectors vs a larger pump and injectors. With the stock pump and larger injectors the a/f ratio was 13.6. With the larger pump and injectors, the a/f is 12.6.