My very fist job in my life was actually making those mock-ups for several products. If you're interested, I can explain a bit on how (usually) works.
When you need a visual design for a product, be it a toy, a balm bottle, a keychain of whatever you first tell the graphic designer to do the first draft (my job). This is also the case for many boxes, especially for special editions. After the work is done, your supervisor check it and give the feedback: maybe is too dark for the target audience, maybe the colors are off, maybe you idea sucks, and so on.
Now keep in mind that at this moment the image is still a photoshopped image, not a 3D render (most of the time; I'm talking about my personal experience), and in rare cases those photoshopped images end to be the actual "official" one. Like
this one (look at the toilet paper), as opposed to
this one. See the difference?
Once the supervisor gives the ok, the process proceed. Remember this part for later.
Then, in the case of a product box, it goes straight to a specific department that make the actual box. I said specific because they are responsible for basically everything regarding the actual box: the colors (if you're familiar with RGB vs CMYK you know what I mean), font dimension (very important if the wording need to be translated), all the box sides, and all those fine prints you see on every box. In this stage the intern can actually make some changes, especially true if you consider that most companies always have some kind of "template" regarding their products. Just grab any box near you and you'll see with your own eyes: the prints, the warnings, the logos, the alignment. There are actual people who specifically work on those, in order to have a good looking AND functional product.
After all that, it usually got double-checked and finally released to the public (and to the physical manufactor). Remember, this process takes place AFTER the actual product is done (or at least should be).
Before proceeding, keep in mind that I worked in a small company and not in a huge multinational, and basically never in a NDA environment. So from now take everything with a grain of salt.
Now, from my personal experience, on this "box theory" I can tell you this. The
Smash Bros Special Edition Box is real, like an actual physical box that has been sent to Amazon, along with a specific serial number (and tons of paperwork) in order to be and actual buyable product. Remember that the ESBR already have the final version of the game with all the characters in it, its basically already finished.
But that box is a placeholder. "Hurr-dur, of course its a placeholder, Isabelle is not on it!". And that's the point.
Remember the supervisor stage? In this particular case, the team already know the full rooster but they get specifically instructed about what characters are going to be revealed to the public, so its up to the supervisor to tell "put all the characters up to the 67°, we are going to send this before the planned 5th september direct" or something like that to the poor intern, so he (and later the box department) have to create a desing with those instructions in place.
If you consider that the Steelbox was
already announced back in august (look at the date), I think its pretty safe to assume that whoever created that box was specifically instructed on how many characters he was supposed to show. So the empty slots are there for a reason, they are not random.
Its interesting to note the discrepancy in the Palutena-Corrin segment, from my point of view it could really be a slip up of an echo fighter there (Ken/Medusa/Ms. Pacman/Zack...), I mean, it wouldn't be the first time Nintendo
screw up like this. But regarding the supposed single remaining slot, I'm pretty confident its a placeholder. As in, the entire grid might change, shrunk, moved, some characters may be on the back and so on.
That said, don't expect 5-6 more unique anyways, Sakurai specifically told us the opposite. There are probably 2 more left, 3 if you want to be optimistic.
Hope it helped.
TL;DR: 90% placeholder, 10% true.
