Set-up the PI with the USB device, then configure the Mint install to also mount the same USB device, but using the Manual method.

When scraping, you'll have to use an external scraper and configure it to save the artwork in the ROM's folder (EmulationStation saves it in $HOME/.emulationstation by default, which is not on the USB drive).
EmulationStation themes will not be transferrable this way, you need to install them on both machines.