the question you post is quite interesting. The point is that the board you are using does not offer HW Timing of digital lines among its features.
This means that Reads and Writes are depending on software function calls.
Being Windows a non deterministic OS as you know, sw function calls get executed whenever the CPU has time for them.
If you look at the metacode you reported above, in the scalar write case, you are calling the same function 3 times. This allows for "asynchronous" writes, that is each digital sample is not tied to the previous one, and the OS can serve other interrupts between 2 consecutive calls.
In the second instance (Array Write), you are calling the Write function just once. This occurs faster than calling the function 3 times in a row, but on the other hand it does not allow the OS to serve interrupts between 2 consecutive digital samples.
Now, if you are looking for performance, either speed or determinism, I suggest you determine what the constraints are for your application and then figure out whether you need an RT OS or a HW Timed digital board.