I read in one of the threads on this forum, that the motivation for the 2.0 mm header wasn't space, but rather to prevent people from getting confused and assuming 3.3 volt IO, where these boards are 1.8 volt.
Frankly, nothing about the header pin spacing implies voltage. Nothing there distinguishes between 3.3 and 5 volt, so why should there be a special size to imply 1.8 volt? It also has proven to be a totally ineffective means of distinguishing, since there is an instance on this forum already of someone hooking 3.3 volt devices onto the 2.0 mm header!
At least they use a full size HDMI plug and not those flimsy micro-HDMI plugs like IFC uses.
The USB issue is more about the SoC than the board design. This SoC only has a single USB port, so multiple USB ports are actually added by including a USB hub IC. Unfortunately, the only way to achieve USB slave (for ADB/fastboot/etc.) is by physically switching the USB pins on the SoC from the switch to the uUSB socket. This is all detailed in the technical documentation.