A get-around has been found allowing the system to boot:

1. Boot the Apple computer to grub, takes about 2 minutes
2. Press a key, then edit your boot configuration to include the kernel command 
line parameter break, takes about 2 minutes
3. At the initramfs prompt usb works fine. Enter command reboot
4. This initiates a graceful shutdown of Linux, and the Apple computer can now 
be booted with usb3 operating normally

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https://bugs.launchpad.net/bugs/1668105

Title:
  xhci_kcd module turns off usb host controller on boot

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