My first question to the operating company is whether that yacht has ever been run aground before.
A Beneteau 40.7 could only capsize and stay capsized if the keel fell off. That could only happen if there was some previous damage to the area where the keel is attached to the hull. The Beneteau First series of boats are regatta yachts and are very susceptible to damage in a grounding due to a deep high-aspect ratio keel which has only a small area to transmit loads to the hull. A keel starting to work loose would explain them taking in water, and being unable to verify the source of the leak since the bilge pumps are inside a pit in the keel area.
They had a sat-phone and if they had time to abandon ship, they could have sent a message, so I suspect they capsized and sank too quickly to get into their liferaft. This would also be consistent with keel failure.
If the photo of they yacht in the Gruaniad is recent, it does not look like they had a fixed EPIRB, which is not unusual for a coastal racing yacht. They probably rented the sat-phone expecting that to be sufficient for their off-shore trip back home.
As for personal EPIRBs, they have very low power and need a stable platform and clear view of the sky to have any chance of being picked up.