I have updated to the latest version.
I realised that I could trigger the sync to the sdcard through the sync options that appear in the main panel. This let me choose the path Windows Phone/sdcard over Windows Phone/phone. However this was still impossible through the menu as in Edit/Prefs/...
MB seems to have difficulties in reading the info from the device correctly (I have 8gb internal memory and 32gb sdcard)?
Let's see what the files will be like once the syncing has finished.
Music Bee 3; EAC; MP3Tag; Music on Synology NAS 115; Logitech Media Server on RPI 3; RPI 2 with Hifiberry; Poweramp for Android/Lineage