low, aft
An isolation tranformer weighs a good seventy pounds, so you want the weight low, but not in the bilges. And you should mount the transformer close to where the shorepower comes into the boat, which means aft. In my 46, the transformer is inside the starboard aft berth, since the shorepower comes in on starboard. A zinc fish won't do near the job an isolation transformer will do. Nor will a galvanic isolator. (For that matter, nor will a galvanic isolator and a zinc fish used in combination.)