Upside down eh? I didn't really pay all that close attention to the ports, but you have a really strong point. The disc drive orientation as well. Phil did say the ports on Scorpio are laid out exactly the same as XB1S, so upgrading would be super simple in terms of just swaping directly like for like and your good to go.
With that in mind, the fact that Scorpio's internal design immediately makes you think of PS4, since ironically enough, its built "upside down" as well, makes this case even stronger. The fan type, a first for XB, but normal now for PS. The internal power supply, newer to XB, normal for PS. The cooling system completely closed in for maximum heat output directly out the rear of the console, newer to XB, normal for PS. Extremely compact design overall, newer to XB, normal for PS. I wonder if the mass storage HDD/SSD is upgradable based on its location inside the console? It looks like it could be potentially, not that its necessary with external support.
Scorpio being built "upside down" doesn't seem all that far fetched now really. The orientation in the picture would mimic Scorpio standing up like XB1S. When Scorpio is lying down it would be "upside down" inside the shell, in comparison to the XB1S, but the disc drive would end up on the same side because of this. Phil did say he wanted a family resemblance between them and this would allow for exactly that. I have a feeling Scorpio is going to be smaller than most think.
Good catch! I think your right.