While the cylinder head combustion chamber volume will certainly be part of equation for determining the Piston Dish Volume, and eventual SC/R, it does not affect or determine the quench dimension.
The quench dimension formula is ..... Piston deck height + compressed head gasket thickness.
Deck height is "0" and a .042 compressed head gasket is used for my .042 quench.
With regard to a 3.750" stroke 6.3L SBC, the Hot Rod guys shoot for a quench dimension of approx .060" .......... but your .042" is very close for a Marine Cruiser build.
If you do a Closed Cooling System, you can use the high grade Automotive head gaskets that will give you more options for compressed thickness.
Engines will run a half closed cooling system, as I want the exhaust manifolds to be raw water cooled to help pull heat out from the heads.
Also, while the Hot Rod guys love the 6.0" connecting rods ..... for a 6.3L Marine Cruiser build, you'll do better if you were to stick with the 5.7" connecting rods.
This wrist pin location leaves the skirts longer.
5.7" PM rods used