mostly, yes. One thing Banks is good at -- reading and interpreting signals on the engine and reacting to them. they have all kinds of cool decisions in the box. for example, they won't fuel until coolant temp reaches 160 degrees. something like that. they get this information from the DataLink / CANbus.
But I would be concerned about level 6 throwing a code. not for a failure, but becasue you don't want no stinkin engine codes on your truck. it shouldn't do that in my opinion. it means that the box is dialing up a greater rail pressure than the ECM is programmed to allow. Did they say to expect that code all the time on level 6?
you may or may not be able to clear the code with the battery trick. they may have tested it succesfully but I wouldn't depend on it. Try the battery trick and then do the three-cycle ignition switch test. maybe it will work.
If you plan to live with a box that regularly sets codes you should either invest in an OBD scanner (clear codes yourself) or plan to visit Autozone. yes they are familiar with clearing codes -- they just come out and hook up their scanner box to your truck and show you the codes. they can't (legally) push the "clear" button but they let you do it
be aware that if the engine light goes out you still can have a code. If you go to the dealer and they see P0088, they may impose a limited warranty on your VIN. without going into the morality questions here, just note that when you go to the dealer, you don't need the additional confusion of an engine code.
ultimately the important thing is that you are comfortable with a plan to manage the codes (how often they occur and what if anything you do about it).