It is quite important that you issue a "sudo closechroot" (or use the icon) before connecting the USB cable for "Mass Storage Mode". The Easy Debian mount definitely interferes with the USB mode.
As for running native partition vs loopback image - there is *much* benefit of doing so. Currently, You're not gaining (almost) anything over keeping image file in vfat. If You actually have files on partition, natively, You're benefiting running whole (Easy) Debian natively (chroot = native). Getting files out/to loopback image is second biggest bootleneck, next only to low amount of RAM.