you can backup everything, but in order to restore a partition, you have to enter recovery mode and access the reader via serial gadget connection. but this is impossible with a damaged boot manager / initrd / kernel
So, I would not only backup the whole flash disk, but each partition seperately because in case of a messed up device, you will more likely want to restore system or data partition
the thread I linked contains a list which explains the purpose of each partition (post #3)
there you'll also find a command line tool you can use: dd
but beware - dd can easily brick your reader without warning...
gparted also has a cli frontend btw...