What year (there are multiple I have seen for sale in NJ)? I just bought an '06 Marlin in the fall for a great price, waived the survey to expedite (4 year old and 8 year old pristine surveys were provided, no delamination). Transom bang cap was in good condition, and no visible wear/cracking on transom. Price was at a place anyways where if transom had to be rebuilt in future, it would still make sense financially (in terms of a boat...). Regardless, no one wants to go through this, so I reached out to Grady as this is really only consistent issue with Marlins, and they advised below, seemed to be earlier models that mostly had the issue. As for your situation, as long as its a reputable glass shop, and the end price is right, not sure why it would be a concern.
"The transom and stringers on our 2006 300 marlin are built with marine treated plywood that is encapsulated with fiberglass. Our earlier boats used aluminum bang plates at the deck to hull joint at the motor wells on our boats. It would not hurt to seal around the corner side trim pieces and bang plate as preventive maintenance.
Our Marlins have a transom brace that runs from one stern eye to the other and has two welded legs that thru bolt through the stringers on this boat. we supported."