I set a transom mount inside my hull on both the Grady that I had previous to the Wellcraft and an old Stamas that I had. Didn't perform well on the Stamas, but I was fairly happy with the Grady application. I think I can attribute the difference in performance to output power of the unit. Most of the units that are available on todays market are of higher wattage than what was available back then and I think the higher wattages give back what shooting through the hull may take away. A lot of the manufacturers today are using the Arimar transducers which are among some of the best made. I'm still trying to make up my mind as to mount my new Garmin (Arimar) transducer on the transom of the Wellcraft or in-hull. The Garmin shows water temp, which I know is only surface temp, but is sometimes useful. You still get a temp reading through the hull, but not real accurate.
On the Grady, I used a cardboard tube cut to the angle of my hull and set the transducer in a bedding of thick two part epoxy.