It's easy to get out into the deep end of the pool chasing the rivet counting aspect this can have.
Which can lead astray as we are al depondent on the accuracy of the hull as moulded in measuring these things.
There are a number of "waterlines" on ships. The one on plans is virtualy always the "design waterline" which can be a 'fiction' in that it's placed to evenly split the body of the ship, the better to fair the drawings in three dimensions. But, usually, some estimation of where the buoyant waterline is represented.
USN is focused on three waterlines in the ship's documentation. One is the fully laden waterline, with all wartime stores, personnel, expendables and the like aboard. The other is the unladen waterline--which is needful to know clearances for drydocking. The other one waterline of significance is the "cruising" waterline, which is the depth the vessel rides in "normal" loading. In addition, there will be recommneded drafts based on stability testing for operations in areas with storms or icing or the like.
Boot topping also varies. In peacetime, it's not ucommon to have boot topping be only 4 foot wide. The lack of depth is less of an issue as ships at peace are kept "topped off" in fuel and expendables, and sledom unload any quantity of ordinance. So their draft seldom varies.
Wartime practice is different. Boot topping can expand to 8 or 10, or 12 feet. Shipe are expected to go out and expend all their expendables and return to a port near empty.
Boot topping typically is laid on as a 1/3 - 2/3 propsition based on an unloaded condition.
Further, USN practice wsa to "even" the boot topping to the nearest 6" tall draft mark. Which is a convenince for the sailor painting the thing while perched on a plank hung off padeye on the hull above (and not needing to have both black and white paint for draft marks is faster to Liberty after Paint Call).
The ship hulls are marked with a weld bead for most of these marking, so that a chalk line or soapstone be used to mark them out.
So, sadly, this is not as easy ans just plopping a strip of 3mm tape down the hull and calling it even.