For the part i understand :
There is the additionnal information of the braking research that is required to compare result, as high braking research increase the maximum throughput due to allowing train shorter braking distance, being closer to each other and thus increasing density even at the same speed which would yield more wagons per minutes.
However, from your "about 325 wagons/min" i suppose you have accounted for braking research as this throughput cannot be reached otherwise. 325 wagons/minutes with 1-20 trains represent 16.25 trains per minutes, which is to my calculation requiring at least braking research 8 ( 1.8 modifier )
https://www.desmos.com/calculator/mrewge9xgq
This throughput can be reached with such braking research and even a little more, but only if the trains are allowed to reach max speed or close, which would only allow 3 of such trains in a square of 100 height and 100 width.
Now 263 wagons per minutes with 1-12 trains represent 21.6 trains per minutes or so for this one braking force research 9 is required and this throughput would require train running at around 238 km/h , which for the same kind of loop would require 4.77 trains, so most likely not possible in game to reach on this amount of track
https://www.desmos.com/calculator/yfxtp8stbh
but a sligthlier larger loop of 96 width and 250 height would get this throughput with 8 trains.
And finally 125 wagons per minutes with 1-4 trains is 31.25 trains per minutes , this one would only require braking force multiplier of 1.4 https://www.desmos.com/calculator/ktrchs6ai2
I suppose this is the test where your prediction is the lowest compared to mine, and i'm afraid i have already posted a save game where a throughput of 37 trains per minute is achieved with 1-4 trains, ( which was done with braking research giving a multiplier of 2) so i have to disagree a little on this one and think something must have slipped in the measure because the other results are closer to the max throughput theorized in perfect flow condition.
My guess is that the train was allowed to go too fast but you had braking research mutiplier 2 https://www.desmos.com/calculator/8zxbpcqj5n
The train reached its max speed or around 250 km/h which correspond to around 32 trains per minutes on a single lane but you would have gotten a higher throughput if trains were going at 160 km/h or so , around 37 train per minutes.
I think your method for measuring throughput is correct, but i think your method to estimate the max throughput is not.
I have some data that log the position ID and speed of 12 1-4 trains in a traffic jam on a square loop Still trying to find a way to import those in Desmos, ideally to graph the speed and position of trains 658 667 694 and so on over the few minutes of recording.
Edit : it appear those data only log something about a train when it is braking and as such it is only the "braking profile" of the trains, the acceleration is not shown.
It would also appear that for train 658, the braking profile repeat itself after 16 occurences of 0 speed. With those it is possible to "math" the speed of propagation of the traffic jam, the average speed of the train during the traffic jam in the stop and go regime, and then compare with the same setup without traffic jam due to signal being spaced closer to each other.
The data correspond to the loop 5 in previous save game