not all those potential leak sources are checkable at sea.
Yes they are. Boats of that construction era all have immediately liftable panels and floorboards throughout the yacht. If you know the boat you can eliminate all causes of likely leaks within a few minutes. The only potential leak which is very hard to confirm/eliminate is a keel bolt leek. So if all the usual suspects have been eliminated, you have to presume a keel problem and act accordingly.
Even if the leak had been traced to the keel, your drill of everyone on deck, sail downwind (where to?)
They were on a West-East crossing of the Atlantic, so somewhere within an eastwards cyclonic depression. i would have lain a-hull with sea anchors from the bow (in a fin keel yacht like that), and awaited the eastern edge of the depression (i.e. northerlies), then headed south to calmer waters, and eventually (assuming help had not arrived) could have eventually picked up the easterly trade winds and gone back to the Caribbean downwind. They would have had at least four weeks supplies on board so could easily have adopted such a strategy.
still leaves them in a sinking yacht, thousands of miles from safety, exhausted and hypothermic.
The yacht wasn't really sinking until the keel fell off. It may have been leaking - but it it had been really "sinking" they would have abandoned earlier.
Nor was your comment about "liferaft buried in a locker" borne out by the US Coastguard swimmer.
I was using the term generically as usually on regatta-oriented yachts the lifreaft is often very inaccessible in either a cabin or deep in a locker. In a cruising yacht it is more easily deployable, either in a cradle on the transom or on the deck in front of the mast, but even so it requires undoing a fiddly "quick" release catch and a fair bit of force to get it out of its cradle (otherwise a random wave could deploy it). Yachts of that size do not have hydrostatic release life rafts.
In a yacht where an experienced crew have recognised that they were expecting an imminent capsize, the liferaft would be loose in the cockpit attached to the yacht only by its trigger line, so if the yacht goes over the liferaft will deploy without having to fumble for tiny release catches which are impossible to feel even in the dark, let alone underwater.
The fact that the coastguard swimmer found the raft normally stowed (whether in a locker or under the helmsman's seat which is usual for Beneteau's of that size) shows that the crew had not realised that hat they had a keel problem and had not anticipated a capsize at any moment.