Regarding leaking around the main hatch idea. It did occur to me that a heavy rain is often associated with a lot of wind and this was certainly the case in February 2020 ( ery wet F8 Gale for several days) when my problem occured
Since KOTO was moored on a marina berth, and effectively held abeam to the wind:
a) the rain might have been horizontal and was driven into the sides of the hatch and beyond; and
b) the boat will also list away from the wind in gusts and allowing rainwater to slide off the hatch into the deck cavity.
Very difficult to replacate this in harbour, unless a another gale occurs, but may be chuck a bucket of water over the hatch when sailing close hauled in a breeze? This could prove/disprove the theory.