Experience is the best and one thing by sanding the hull first off helps to give you more of a flat surface. As for the gel coat it too had air bubbles probably from the application of it in it. That was another reason. As for the location of the depth finder, well there is only one place in the water ballast boats and that generally is under the rear berth adjacent the bilge pump. Do not even think of drilling thru the ballast tank as that is the dumbest idea of all. As for attachment I have tried all and of course the best is thru hull but there are ways to get around it. As for application of attachment using epoxy, plumbers putty, 5200/4200, emmersion methods inside the hull and so on, I like the plumbers putty and it works. With anything though you have to make sure there are no air bubbles when attaching inside in the epoxy, plummbers putty and so forth. The use of epoxy I never even suggested. It is heck to get off first and what if you make a mistake and there are air bubbles between the transducer and hull? Not so good and cursing. That is why.
As for the water bag trick and you do get a reading, suggest placement there. I note petroleum jelly was used but when cleaning that up, you have to make sure all of that is cleaned up or adhesion will not take place. PS Plumbers putty was suggest by a member on the production line as to attachment many years ago but did not think that was viable. I was proven wrong by those who did use it.