I think that the voltage changes as you switch alt on and off will do funny things to your tune. Delivery of bang juice changes with voltage to the injector, the haltec PS use a table to compensate for this, do the factory ecu's do this? might be a big enough difference at big rpm/ load to make a difference, or at worst, do damage. Your voltage at the injectors will drop about 1 volt without the alt running, worse with a shit battery, lights on,doof box at full noise etc.....
Just a thought.