One reason they recommend a thru-hull transducer on an in-board is turbulence. On a boat with an outboard, the props are aft of the transom. But on an inboard, the props are forward of the transom and could cause water and bubble turbulence to screw up your readings if you mount the transducer in the wake of the props. The sonar will get dispursed by air bubbles in the prop wash.
If you go with the transom mount, first take your boat for a cruise and observe the water as it passes by the transom. The darker the water the fewer bubbles. Mount it there. That's where you will get the cleanest water and the best performance.
Peter
1981 32' sedan bridge
twin Chrysler 360 cu. in. 250 hp engines
Raw water cooled
Nimbus II
Home port: New Buffalo, MI