If I remember correctly the stated reason was to prevent power conflict from a powered USB device.
(I thought the Usb cable spec provides protection?)
This really does not make sense to me.
A powered USB device does not send power back to the USB port it is connected to.
It must be something else - I don't think about something fishy, they must have a valid reason, it's just that I don't see it now.
Looking at a Dell monitor with a pair of broken USB ports, the USB 5V in only goes to signal its presence and power to the monitor's usb ports is supplied from the monitor power supply. If you look at the inexpensive 7 port USB hubs available now the 5 volts from its supply is common with the 5 volts on any line in. Plug one of those into your BBB board, then mistakenly plug in a 12vdc wall wart with an identical connector as the USB hub's power supply and you have 12vdc heading up into your BBB attached to the Jupiter.