One thing that you might have missed given the deluge of information coming at you regarding the Super NES Classic Edition, was that those SNES shaped controller ports are actually just for show. As shown in the photo of the Japanese version, you can clearly see the panel pops out and unveils two Wii Remote style ports (which is the same as the NES Mini).
We'd like to think that the eject button is used in some way to help make this process easier. Time will tell.
If you need a reminder of what these ports look like, they're the same as those used for the Nunchuk / Classic Controllers on the Wii Remote, and you can see how they looked on the NES Mini below (though they'll have been rotated 90 degrees on the SNES Mini).
For the time being it is a mystery how the North American controller ports are revealed. We're guessing that the fake controller ports will slide either to the left or the right separately from one another.
We're also not sure what the mysterious hole is for to the left of the fake controller port on the North American version. [Update: Apparently this is the power light, excuse us for being so British]
Let us know your theories on how all this might work in practice with a comment below.