What color is the car? Certain colors (esp metallics) require adjacent body panels to be 'blended' in to match properly. BMW's CPO checklist does NOT disqualify for having paintwork. The whole car could have been painted. It could have been in an accident. As long as it is repaired to BMW's standards, it can still be CPO. In fact, the dealer may have had the work done! In fact, the rear bumper was likely resprayed by/for the dealer as cosmetic reconditioning.
I say get the panel alignment corrected, and don't sweat it.
http://resource.bmwusa.com/pdf_988f0bce-f3e2-44ac-a143-a81cd9e87fc2.arox