I would imagine we could get a proper fuel level measurement quite easily using a properly measured carb. I would probably do it like this:
Temporarily add some kind of vertical strip (paper or something else that would change color if soaked) up the inside of a bowl that would indicate the highest level reached by the fuel. Attach the empty bowl (with strip), turn on petcock, let bowl fill completely, turn off petcock, empty bowl using the drain and then remove bowl. Wouldn't the highest level indicated on the strip correspond to the correct fuel level? Who knows, maybe even a magic marker line would work (if gasoline wipes away the portion of the line below the fuel level).
I am assuming that HondaMan, or whoever arrived at the 4mm fuel level measurement, did it somewhat like that.
By the way, I do have a Clymer's manual, but it's not with me right now. I'm currently staring at the Honda Shop Manual and it does not show the fuel level, it only shows how to set the height using a gauge. I do find it interesting that the Clymer manual is deemed "correct" for something debatable like this, but "unreliable" for so many other things!
Edit: My method above assumes that someone doesn't trust the "clear tube" method as being an accurate indicator of the fuel level inside the bowl. If we agree that it is accurate (not sure why it wouldn't be), then forget the strip and all that nonsense. Just get a properly calibrated 26mm carb and use the clear tube to measure where the fuel level is relative to the bowl top surface. Then you can use that same measurement (4mm or whatever it comes out to) as a guide for any other carb. Amiright?