Generally, I am in favor of making UI/UX elements consistent when possible. In this case, however, I think the "problem" of 2-D versus 3-D elements is a bit of a red herring.
I haven't seen evidence that people are confused by the fact that the inbox icon is 3-D while the achievements graph is 2-D. Rather, the confusion is caused by the fact that the inbox tray is, at this point, a somewhat antiquated and therefore unfamiliar object. (If the only misinterpretation of the inbox tray was that people thought it was an envelope, we'd be fine, since that's another common metaphor for "inbox", but as the questions you linked to illustrate, some people can't figure it out at all and others have a wide variety of interpretations.)
Regardless of whether the issue is one of dimensions or one of a poorly chosen symbol, I actually don't think it's a pressing problem to fix. Even in those threads you linked, people clearly understand the function of the icon, even if they like to debate what the symbol actually is. Sure, we could make it prettier or a more obvious illustration, but since people know that it's their inbox, and that they go there to see replies, there isn't much of a real problem to solve.
As far as why this design decision was made...we needed an icon that was small and recognizable in black and white. Our designer decided to go with the inbox tray symbol (there was some discussion about using an envelope, but I can't recall if there was any reason other than personal preference for going with the inbox tray), and arrived at what you see on the page.