ok - hi ya - I think you are being too cautious here. A bit beyond yourself by too much thinking and not enough making
if you look at your sketch number 1 and you have fitted all your stringers, all your keel and everything and you have skimmed the hull with plywood or whatever; your outer skin should be proud of the top of your frames/bulkheads. Allowing you to fit a deck in to which you will have to what is known as scribe the deck in.
Doing it this way and not taking the thickness of your deck off the top of the frames; will leave you a model slightly higher - in other words the thickness of your deck.
Now, on your 2nd pic - doing it that way -
what you would do is build your hull, frames and so forth and apply your outer skin of the hull and then sand the top of the skin flush with your bulkheads/frames. Then apply your deck on top of it.
Then, sand your deck to the shape of the outside of your hull.
This again, if you don't remove the thickness of your deck from the top of the frames you will be left with a slightly higher hull.
If you read either the Spashette build or the Cervia tug build, or RAF 64 FOOT launch in the masterclass builds on this forum, you will see how I use method 2 of your drawings. I find this one of the easiest ways.
john