There are actually two ways to measure a stem.
First, there is the drafting-board, center-to-center-on-center method that puts a number on the actual center (bars) to center (handlebar) along the centerline of the extension.
This is mostly used today, since the demise of race-quality quill stems, and was almost universally used on Japanese stems (but for a few of the higher-end ones).
The second method better suits the needs of field measurement, perfect for determining what stem length is on the bike without having to withdraw the quill from the steerer as is usually needed to find a number. This method is done by laying a ruler or tape measure across the top of the stem's extension and measuring from the center of the expander bolt to the top-center of the clamp (the tangency point where the ruler touches the OD of the stem clamp.
This method applies to racing stems like Cinelli, ITM, TTT and to certain top-level Japanese quill stems, such as Shimano's Nitto-made "aero" stems (which accept 26.4mm bars BTW).
The difference in measurement methods means that a typical racing quill stem is 4mm or so shorter than a same-sized (designated size) Japanese stem.
This difference arises from the vertical distance from the stem extension's centerline up to the top of the clamp and quill bolt, up along the canted quill axis, which makes for a larger measured dimension when laying a ruler across the top (field measurement method).
I agree that it can be a bit of a dilemma coming up with the right stem and bars for a particular quill-stemmed build. Being as there are potentially four clamp diameters and three quill diameters, on top of having to find the right extension length, I have to keep a stockpile of parts on hand.
I like these stems, which I've found only in 60, 90 and 110mm extensions and with reduced 21.1mm (.833") quill diameter.
