If the stack gets very hot, what does it come into contact with as it passes thru the deck?
It does get pretty hot, but not as bad as it would if it weren't a double-walled chimney (intake air comes down the outer perimeter, exhaust goes up the inner flue). Where it exits the coachroof, the hole diameter is cut so that there is a 1/4" gap between the flue and the deck material. I stuffed some flameproof insulation in there, but I think the air gap alone would be sufficient insulation.
The top of the flue terminates at the flue cap, which slips over and covers the top of the chimney, and holds it centered in place via some feet that splay out and screw into the deck or mounting block.
In a squall or a roll does that cover make for a watertight seal?
In a squall, yes. In a roll, no.
The flue guard (which fits over the flue cap) not only protects the flue cap from sheets, but also has a shield to block spray taken over the bow. We have never had any water make it down the chimney.
In a worst case, water could come down the chimney during a roll, but it would not flood the boat since the combustion chamber is sealed to the interior. Probably wouldn't be good for the heater, though.
Fortunately, there is a simple remedy for folks heading off soundings. The flue guard can be removed and a 6" stainless mixing bowl and gasket can be easily fitted over the flue to make it watertight. But then you can't use the heater while it's sealed up....