Tthe ride's computer will not allow for a train to do a "fly-by" through the station. It will shut itself down if the situation were to start happening. With the station speed being so slow, the train would stop in the station.
The topic that arose was the possibility of the train doing this due to spacing. Spacing is controlled by the computer (unless in manual mode which is run by maintainance). If the next block is occupied, the ride WILL NOT send a train. Now for those who are not familiar with the "train block platform", here's how it works.
1) When running 2 trains, there are 3 blocks. From the station to the MCBR is block 1, MCBR (Mid-Course Brake Run) to the final brake run is block 2, and from the final brake run to the station is block 3. When one train leaves the station, the system will not allow another train to exit the station until the first train has passed/arrived at block 2 (MCBR).
2) When running 3 trains, the ride now has 4 blocks. In addition to the same 3 as with two-train operation, block 1 is split into 2 segments: lift hill and post-lift hill. With this operation setting, you can send a train as soon as the previous train leaves the lift hill. There is what we call stacking where one train is in the station, the other is on the transfer track, and the last is on the final brake run.
Now the only way that the ride can move "past" the station and stop is if it is on the lift hill and there is a ride malfunction or if there is a feeder wheel setup. The feeder wheels are the mechanisms used to transport the train from the station to the lift hill. If one of the 5 (plus quick queue when the button is on) operators release their "ride enable" buttons while the majority of the train is on the feeder wheels, the ride will shut itself down; causing a feeder setup.
As you can see, the idea of the train "passing through" the station is not only near impossible, but it is also not a matter of spacing whatsoever.
Lastly, had the train gone through the station (somehow), you don't the ride ops would've stopped the ride? There's a magical red button labeled "E-STOP"...
Just my .02..