The passthrough mode works like it does in vanilla NoLimits 2. The "Station passes" field is exactly the same as the vanilla Station setting "Passes", but I had to include it in the generator because NoLimits' API doesn't expose that value, so the script can't read it.
That said, the number you input in that field is the number of trains that will pass without stopping between each train that will stop.
That setting is normally used for cases where you have several stations acting in sync one after the other, like, for example, on Maverick, or in the virtual world, Journey to Agartha.
These have two stations that dispatch together two trains, therefore, one train 1 dispatches from station A and train 2 dispatches from station B, train 2 will go through station A, but we don't want it to stop and do the station cycle again.
Going one train back, train 3 will advance from before and will go through station B, but we don't want it to stop in station B, but in station A. Therefore, between train 1 and train 3, the two trains that need to stop in station A there was a non-stopping train. The passes value should be 1. The same goes for station B.
If you had 3 stations instead of 2, you'd have 2 non-stopping trains between each stopping train.
Of course, a normal station wants all trains to stop, so there should be 0 non-stopping trains between each stopping train, which is the default value of the passes setting.
Now, the extra thing is that I allow you, through an extension script, to disable a station and make it always behave in passthrough mode, but that has very little to do with the Station passes value (other than the passthrough mode itself, but the activation is different).
So, unless you're referring so something else or specifically want some behaviour that can't be done with a simple pass count, I think the passes setting should be behaving as intended.
In any case, I'll think about the first suggestion in the first paragraph because I find it interesting anyway, but as with everything, no promises on delivering it soon! ;)
If I did not understand something or I did not explain something well enough, don't hestitate to answer back!
Cheers,
Dragón Groar