Best practice for backing up /data/media?
I recommend directly copying files from/to /sdcard.
The sdcard service will handle all the permissions and SELinux contexts for you.
The /storage/emulated/0, /mnt/shell/emulated/0 and /storage/emulated/legacy are all shadow reflexes of /data/media (typically /data/media/0). In the /init.rc file you can find out that the /system/bin/sdcard is a service that controls all of them, so you can just copy the files in /storage/emulated/0 with ease. All other directories like /sdcard and /storage/sdcard0 are symbolic links. They don't matter at all.