The new boats have a better drain setup that deals with this. Yes, you can drill through for a drain. Bearing in mind that the floor of the compartment overlaps the lip of the hull below. That is, a hole through the rear of the transom locker will not drop straight into the engine compartment but onto a lip that runs around the whole hatch area. At least that's how it is on our 05 348. Ours has a couple of small holes inside the locker that let the water drain down into this lip. The lip has another drain that goes into the bilge, to be pumped out if it collects much. What bugged me on our 348 was there's no drain in the rear cockpit seat locker. I put one it. It was a bit of a job as the platform the locker rests upon is a LOT thicker than you'd imagine. I had to use about a 4" extension to get through the deck into the engine compartment below. From there I tied into the drain lines used for the two lockers on the swim platform. Now when water gets into that locker it drains right out.
Any time you go through any part of the boat you want to make SURE the through-hole gets SEALED. You do not want water to get in around whatever gets installed. Water will soak the material inside, swell up, cause blisters and all sorts of trouble. The most common recipe is to drill the hole slightly larger, cap the bottom of the hole, fill it with epoxy and then re-drill through that to get your desired hole size. This way it's the epoxy up against the inner layers of the material, not just an air gap or poorly applied sealant.
The latest models appear to have changed the slope of the floor in that locker (slightly) enough to allow draining out on to the swim platform through some stainless drains. Not sure if there's an easy way to retrofit this.
My suggestion, get a a hold of Four Winns directly with your concerns about this. They may be able to work with the dealer to correct it.
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