Thanks all for your comments! I for sure picked up a few ideas and feel better moving forward. For the curious this is what I've decided on:
Potable drinking water hose inside of old fire hose to keep water cool and protect from the sun.
An easy to access ball valve at the end of our finger pier to shut off the water when we leave.
A filter (probably just sediment filter outside).
A gallon / flow meter that can be set to shut off after 200 gallons.
Hopefully the filter and waterminder / shut off meter can be installed in a battery box (water lines in and out instead of battery cables) that can be painted to protect from UV.
At the boat a SHURflo pressure saver water entry.
Inside the boat and BEFORE the fresh water pump a 3 way valve with a limiter screw (probably just a wood screw stopping the handle from turning very far).
To fill the tank the valve can be turned a bit to back flow into the fresh water tanks. I can also remove the fill caps and turn the water on at a higher rate - hopefully helping to keep sediment from piling up on the bottom of the tanks. (My tanks have decent access ports and I already cleaned them out. There was years of stuff on the bottom including some big rust bubbles where the baffles were welded. All pinhole type leaks I've encountered in the past appeared to be a result of corrosion under gunk / sediment.)
Once the tanks are full I just turn the valve the other way for unlimited water in the boat.
When underway the valve is turned to open the lines from the tanks instead of from the city water. It will be easy to remember because there won't be any water coming out of fixtures until I do it.
The freshwater lines from the tanks and best place for the water entry happens to be under the galley sink so this all works out.
I'm already in the process of upgrading the bilge pumps.
I thought of a toilet ball valve bluevee but I had a hard time figuring out how to install it and I'm not sure they are completely potable as there is a lot of plastic involved. I can imagine a frame to hold the float valve and an inlet line to the top of the tanks where the city water could be attached. But there isn't room for that on any of my tanks and I don't want to mess with the cabinetry
HopCar, the waterminder type gallon meters look kind of cheap but they are specifically for potable water. We have a good carbon filter for drinking water but if I can cut down on how much plastic we drink I'm up for it.
As was mentioned, once the tanks are full I can just switch to city water and won't need the 'autofill' for the tanks. We use the boat more than once a month so hopefully sediment (in the fresh water and fuel tanks too) will get suspended and flushed out. Running the freshwater pump long enough to pump out the tanks entirely will take a long time. I think I can remember to do at least one tank a month (we have three) and that will be enough to keep everything fresh.
Whew! Now I just have to buy the rest of this stuff and install it!