The author of the article seems to be confusing or blurring "military or 30 minute rated power" as they are not the same thing. and "not over boost (roughly "war emergency power" in U.S. terminology)" is also a bit confusing.
For an example see:
http://www.zenoswarbirdvideos.com/Images/P-39/P39SEFC.pdf
The 1000hp at 2600rpm and 39.2 in is the "Normal" or 30 min rating (actually US engines did not usually have a 30 min rating, it was often either 60 minutes or until the fuel ran out=max continuous)
For this engine the next step is "military power" 1150hp at 3000rpm and 44.5inches. In this case it has a 15 min rating but many US engines had a 5 min rating at MIL power.
Next step is the "take-off" rating, in many cases it was the same as "Military power" and is usually 5 min. The use of MIL or T-O power triggered NO EXTRA maintenance procedures and instances of use were NOT logged in the aircraft's records. In this case it was allowed to use 1200hp and 50.5in of boost which is certainly "over boost" compared to Military power.
The WER rating is 1420hp using 57in of manifold pressure.
As an example of how terminology changed see:
http://www.zenoswarbirdvideos.com/Images/B-25/B25SEFC.pdf
Please note there is no "military" or WER on the chart. But the "Maximum Emergency" rpm and manifold pressure and power output are those of later R-2600 engines that have "Military" ratings. Again, please note the time limits and please note that "take-off power" required more "boost" than MAX emergency power, by roughly 50-75mm.
This is just different terminology by the US Army depending on the date in the war. Trying to compare to other countries rating systems or procedures can get really difficult. The British used the 30 minute rating and I believe the Germans did too. I don't know if an engine that can go for 30 minutes at power level XXX can go longer or if it introduces wear problems. ALL these power levels were subject to temperature limits. exceeding oil, coolant, or cylinder temperature would call for throttling back regardless of the time limit.
Many engines were Throttled to less than full power for take-off in normal conditions. Being able to "overboost" in difficult conditions for a few moments or even several minutes is not quite the same thing as a WER setting.
I do not disagree with the fact that the tests of the Zero with less than full rpm and boost do not reflect it's true performance but I do have strong reservations about the "terminology" used.
As in this sentence. "Sakai distinguished between normal full power speed (316 m.p.h.) and over boost (345 m.p.h.)."
In US use "normal full power" can mean the MAX continuous rating, which in the late 1930s was considered the engines "normal" rating.
You are NOT going to pick up roughly 10% in speed by increasing the manifold pressure by 8.5%. For instance if our plane needs 1000hp to do 345mph it will only need 742hp to do 316mph.
Another problem with this article is that it fails to take altitude into account. The Sakae 21 engine used a two speed supercharger instead of the single speed of the Sakae 12.
Zeros with Sakae 21s were deployed into combat areas in the Spring of 1942 which makes depending on combat reports to confirm the speed of the Zero 21 a bit of a problem. How did the F4F or P-39 pilot KNOW which engine was in the Zero he was chasing or was chasing him?