If there were an USB3 hub in the lower part and all interfaces like SD card readers, audio connections, modem, keyboard, external USB ports, all these need specific USB converters connected to the USB hub.I think only HDMI would be better on upper part, all the other, as they are not super fast (SD card interface used in Pyra is no that fast) can be combined in USB 3. Even could would be place for a M.2 drive on lower part, and that could speed up data even using a USB 3 for comms, compared to SD cards.
With the current design all these are directly connected to the interfaces of the OMAP5 (or future SoC - and all have multiple interfaces for exactly these interfaces).
So using USB3 to interface everything to a SoC adds chips and cost. And it needs space in the lower part for all this.
Yes, we can not change past. These design decision were also based on availability of components in ~2014 - I don't know if there was a cheap and easy to use USB3 hub chip available at all? And there was not even some USB-C standard.
But if you want to design a Pandora 3 or Pyra++, the fundamental architecture can be reconsidered again. But then it is a completely different product/device and not a new CPU board for the existing Pyra.