Word to the wise, Pwiz: Recently Randy Pitchford did a Q&A on Kotaku. A few people brought up the subject of golden keys and the editing of the .ini to acquire a near infinite amount. His responses basically boiled down to this one quote: "Yup - we're fixing the bug and might punish cheaters."
Not sure if that will even effect how the trainer works or how they intend to determine 'cheaters' but definitely be prepared with some backup savegames to test golden keys whenever the game gets patched.