For holes I've become very fond of JB water weld in the stick, make a wad of it, press into the hole and create a mushroom on the inside. I suggest you clean the area well and then wipe down with a solvent before filling the holes. Once cured the JB ww sands super nice.
Uh no hammering on that seam dent, unfortunately it is what it is at this point, pounding will only make it worse in that location causing a leak potential to repair. After my third boat I've come to the conclusion that old tin will never be perfect once it's been dented, bashed or mauled. In that location it will be hardly noticeable once painted and everything else is going on back there on the transom. If someone besides you even notices it I would be surprised and there will be so many nice things to draw the eye too.