I'm with Dean62. View of those decks will be extremely limited, and any change in the plank pattern will be virtually unnoticeable. It really come down to you. If it's worth it to you to match the lower deck pattern to the upper one, AND if you can access the lower deck without too much effort, go for it.Looking great Paul! I'm not sure I would change the lower deck boards, It will most likely be overlooked by the completion of the build. You would be hard pressed to see in there, without leaning over the ship. I'm sure between the masts, yards and sails being in the way, the case you will ultimately build will prevent that. So if you do change it, it will be for your benefit, because only you will know.
As for the master ship builder...throw him overboard, he is impeding progress!!!