Usually a dealer won't check an ECM.The ECM is read throught the OBD II port during state emissions inspection. If no check engine light is on you will be fine. If is was a dealer warranty issue that you brought the car in for like a head gasket, they will able to read stored trouble codes like overboost and if the injector pulse and duration have been altered. If this is a concern get another ECM to Mod and leave one stock. Depending on the dealer you might have problems with the needswings intake because that is noticable just on inspection. It is really more dependent on each dealership, what the problem is and how hard they feel like digging, if they want to get out of warranty work