I have a transom mount simply because I had no other option.
Only way I was goiing to get a thru' hul lto work was to dril la big hole i nthe floor, and fit it in the watertight compartement betwee nthe underside of the hull & the floor. That of course adds another couple of leak paths to the floor cavity...... Hence I wrent transom mount. Took me 4 goes to get it to work almost reliably (probably drops out about once per trip in really lumpy stuff but at moments like that the depth is usually big & irrelevant! It also throws up a ton of spray (to the point I am fabricating / prototyping a small deflector plate to sit above it)
If yo ugo transom mount, one idea is to get a block of wood, and glue it to the transom, so you can screw the sounder to that which means you don't have another two (four?) holes in your transom below the waterline. I used Sikaflex, and 3 seasons later it's still attached.
Another handy thing is that by essentially jacking it backwards by something like 1", it can be raised quite a way when compared to the installation instructions, thus potentially taking it a bit further out the way of potential Impact damage from solids you might run over.
If you do that it;s worth fettling the block of wood with files & sandpaper to look good before installation - I then painted mine with International's "Rescue Orange" epoxy paint to match the hull, which also improves the look.