When withdrawing items through a Terminal or Item Hopper, the smallest stacks should be used first. This prioritizes freeing up inventory slots as much as possible.

To demonstrate what I mean, you can:

1. Start a creative world
2. Place a chest and connect a simple terminal to it
3. Add 96 dirt to the chest through the terminal
4. Inspect the chest. You will see that it has 64 dirt and 32 dirt.
5. Using the terminal, withdraw half a stack of dirt.
6. Inspect the chest again. You will see that it has 32 dirt and 32 dirt.

Despite now holding exactly one stack of dirt, and nothing else, the chest has 2 slots filled out of 27, 25 free.

If the withdrawl would take from the smallest stacks first, the chest would have one stack of 64 and 26 slots free.