I think you’re over, thinking it. If you measure to the top of the threads, call Sam’s and they will tell you what the proper one is for your measurement. As far as accuracy of the gauge and what’s left in the tank when it reads zero, that’s not something I would ever trust the gauge for. Even in modern airliners we still use time flown/fuel burned as a double check against what the fuel gauges read. It’s a requirement and has saved many a pilots and passengers ass. I know other people on the forum have removed the fuel gauges and took the time to add fuel while marking a dip stick. Excellent technique but takes a little time to stick the tanks on the fly.
I personally filled my tanks as full as I could then went on a long trip using the boat as I normally would, hull speed, generator running and the every few hours throttle up for carbon burn. First chance after a number of hours run and on multiple trips for accuracy I filled the tank back up and just did the math. Time run vs. fuel burned. Distance doesn’t matter because wind and current will change, but a throttle setting and the time it’s been at that setting is constant. I’m assuming since you have a motor yacht you’re running at one particular speed, maybe hull speed. Use this method to get an average fuel burn, mine is around 10-12/hour but I plan 15 and there in is my reserve.
I would never run these tanks down to even close to empty. Mine never go below 1/3. I’m sure there’s a ton of crap at the bottom of these tanks that won’t play nice with the racors. The other issue is the generator. I’m going to assume that there’s a standpipe that won’t allow the generator to run the tank below a certain level assuring you always have fuel for the main power plants.
Hope this helps. I am by far no expert on these boats but I’m learning.