Are you aware how long it takes to scan a full device with a sizable library over MTP? You'd want MB to do this every time you connected your device?
I agree with phred, by slightly adjusting your own process - rather than sending things the way you are, adding things you want on your phone to a dedicated playlist and removing things you no longer want from that playlist, keeping that playlist synched to your device, and displaying the playlist column in your Musicbee layout - this can be achieved with much less overhead and no work by the sole developer of Musicbee. It is, maybe, one tick less convenient, and in return you get what you want.