Backup of internal and SD storage via script (USB)
As most of the time: error in layer 8 of OSI model. Here is what I did and what I should have done:

What I did

I mounted my target external drive using sudo (nothing wrong so far) and thus only root has permissions to write, rsync failed to do anything (which makes sense after all) - even when running using sudo.
Where exactly the error was, I am not absolutely sure, but let's focus on 

What I sould have done


Mount the external device using the GUI tools (for I am using an encrypted external drive)
Create a directory in the root of the external drive and chown it to your designated user (or group or both)
Run rsync


I created a small script to automate the finding of the gvfs path and rsync to external drive:

#!/bin/bash

PHONE_VENDOR=0000 # your phone vendor here!  
USERID=1 # your user ID here - possibly `id -u`

PHONE_BUS=\`echo $(lsusb -d ${PHONE_VENDOR}:) | cut -d' ' -f 2\`  
PHONE_BUS=${PHONE_BUS}%2C
PHONE_BUS=${PHONE_BUS}\`echo $(lsusb -d ${PHONE_VENDOR}:) | cut -d' ' -f 4 | cut -b 1-3` #extract vendor ID from lsusb  

SOURCEBASE=/run/${USERID}/gvfs/mtp\:host\=%5Busb%3A${PHONE_BUS}%5D
TARGETBASE= # your target base path here

rsync -a --progress ${SOURCEBASE} ${TARGETBASE}  # your rsync commands here


I don't know if anything changes (or this script works) when applying an fstab entry and then mounting via shell and not relying on the GUI tools.

This works for me and provides a neat way to backup contents from Android phones without copying whole SD-cards or internal spaces.

UPDATE - First real attempt

During execution rsync started throwing I/O-errors, probably because the process in general was taking very long (got about 50GB to sync). I am now starting over.
It might be a good idea to start a foundation by manually copying all files initially and all further syncing-processes by using rsync.

UPDATE - Second attempt

So it happens this amount might be too much for one attempt. Maybe this is my crappy smartphone, too. In general it works and after the first initial load-up it will be fine, I guess.