As of December 30, 2016 a simple automated method was added to run roms from a USB drive.
First Update the RetroPie Setup Script
Re-Enable the USB ROM Transfer Service
Format your USB drive to FAT32 per directions above
Create a folder called retropie-mount on the USB drive
Plug into Raspberry Pi
It will proceed to automatically copy the RetroPie folder AND all of its contents (you may need to reboot to start the copying)
NOTE if you have a large ROM collection already on the SD card it will copy all of the ROMs too so make sure your USB is large enough. It is easiest if you haven't added any roms yet.
Once the folder structure is copied over the USB will be mounted over the RetroPie folder so any ROMs you add to your pi will be run off of the USB.