I don't think that there is a definitive answer, as you see all varieties.
I think it depends on the design of the boat/rig.
Some chain plates are inboard, even on old wooden ships, and run down to the keel in some cases.
Some pass over a board, called a channel (see USS constitution). I am guessing this allows access to the rear of the bottom dead eye (which is outboard on some ships), as you could not thread/tension the rope through a deadeye pressed against the hull. But the gunwhales on an old warship are much higher than those on a smaller fishing vessel.
If the bottom deadeye is above the gunwhale then having the chainplate flat against the hull would not be an issue.
This then comes back to the size of vessel answer. The only way to be correct would be to find drawings or photos of the boat/ship that you are modelling and follow the original design. Not always possible, I know.