Hey KB,
Yes, the transducer supplied is primarily for external mounting, however, most (if not all) jetskis use this transducer that is epoxied inside the hull but you will pick up some "noise" -normally surface clutter and loose some quality.
The "shoot through hull" transducer is an additional R1200 or there about and it is not flat and oval but round (almost like a D cell battery).
I use the Lowrance Elite 5 a have the normal transducer epoxied in my ski internally as I do not like holes etc in my hull. If you use the factory settings the quality and noise on the fishfinder is definitely more than usual, but if you correct the settings, reduce sensitivity etc you get 95%+ of the quality you would on an external mount.
Also, I have "tested" the water temp by comparing it to boats with external transducers and the water temp reading is only out by 1 - 3 degrees at the most.
I believe it 6 of the one and a half a dozen of the other when it comes to mounting your transducer internally or externally....
Johan