Not gonna matter. When sound travels between two different media, the amount of sound energy that's reflected (instead of transmitted) depends on the density difference between the two. The smaller the density difference, the less energy that's reflected (so the more sound energy that's transmitted to the target media - the water in this case).
The density of paint, finished fiberglass, and water are close enough that it has a negligible effect on the efficacy of sonar. That's why you can mount a transducer embedded in epoxy on the inside of your hull, and it'll shoot through to the water just fine. The epoxy, fiberglass hull, and water look almost like one continuous medium to the sound waves and you get ~99% transmission.
OTOH there's a huge difference in density between air and water, and air will totally disrupt your signal. So you want to mount the transducer in a location where it won't break the surface, and won't occasionally get air bubbles underneath it. That means if you mount it at the stern of the boat it should be low enough that it's completely submerged all the time. And you want to avoid mounting it behind rakes and thru-hulls which might trap an air bubble behind it (right under the transducer) at speed.
And Airmar probably recommends putting antifoul paint over the transducer, because a barnacle shell growing on it is going to have a significantly different density than the water.