1. 401a pleb so not sure, but regular cruise control is completely unaffected
2. Yes sir I just keep it in normal mode. No more need for sport since this is like a lovechild of stock normal and sport modes. I'm actually waiting for an answer back from Livernois on whether or not it impacts other drive modes, since they stress avoiding towing with a performance tune. I'll report back once I get an answer.
3. Running with it off requires the entire reflashing process which is a little involved, requires a little underhood action. Day to day there's absolutely zero reason to want it disabled though. Driveability/transmission management is objectively better than stock. Only time I'll even consider flashing back to stock would be for warranty work diagnosis.
4. No screen/app. You can, I just haven't gotten around to it due to my wife's totalitarian dictatorial demands over my time lately. I'm getting bitched at for being "probably on that damn truck forum again."
5. Yes. You upload your truck's specific stock tune to them then fill out a request form that includes your personal list of mods which they can apparently account for remotely. I've noticed the tuner they send does have datalogging features which I haven't explored but imagine could also be sent to them for further finetuning. There's no charge for additional tune requests if/when you get new parts.