Maybe my views may be misconstrued but I have two of a bunch of Amiibo's (not all), one for opening and one for keeping in the box. As a collector, I love the box. As a video gamer, I want to use the thing. Let's be real here, if Nintendo let me use the Amiibo in the box, there would be no point of me owning two. However, that's not the case.
What I can tell you, is I have never bought two of the same amiibo from the same store. I have worked hard to get my doubles. For instance, I had an Ike and a DeDeDe. One, the Ike that came had a busted box due to TRU shipping. Nintendo World was selling wave 3 this past Friday, line ups starting at 8am. My friend and I woke up at 5:30am, took the train down, and waited for over an hour in the frigid cold. My feet are still frozen.
Now, that being said, should I be denied another Ike because I have a dented box one even though I woke up early and did my due diligence? And now, I can open one of my Ike's to use in Codename STEAM, and one for collecting purposes.