Transom mounts for xducers are great if you get them in the right place for your boat. If they are in a stream of bubbles, they will not register correctly or at all. A good model will tell you all that stuff in the installation manual. What's nice is that every mount I've seen give you room to make an up or down adjustment til you get it right.
I had bad luck with my transom mount on a fiberglass boat (stopped reading when I picked up speed) so I moved to a thru hull. In that boat, I was able to mount the thru-hull xducer in the bilge and shoot the sound waves right thru the hull. It was carefully bedded in ordinary silicone laid down slowly so no air bubbles formed. What you saw above in one post is that there is a possibility you could do that in our aluminum Marinettes. Airmar can guide you.
And if you do go thru-hull, I would urge not to use 5200 sealant. It is almost permanent. There is a solvent for it but I don't think every marine store carries it. 4200 will be fine for bedding - flexible and removable. It is used just to seal out water, not hold the thing in place. And if you use a metalfixture coming thru the hull, make the hole big enough so that the metal doesn't contact aluminum. We all know that is beddy, beddy bad!
Joel Albert, Potomac MD
"Charlie B" - 1988 32' FBS
Twin 318's/FWC/16x15 nibral props
docked Deale, MD