The 'factory' depth finder in our '99 E22 is a Lowrance, and it has an internal transducer that mounts on the floor(hull) of the boat on the starboard side just to the right of the stuffing box.
I'd recommend that because it's easily accessible there, will make the wiring simpler, and most importantly, will eliminate having to punch any holes in your transom for the wiring or mounting screws. It seems pretty accurate, and always seems to work, so I don't know of any reason of mounting it outside(unless you have a temperature pickup and you want to know what the surface temperature is of the water.