It changes how the trim operates specifically for FFB devices. The special option essentially makes it so that the trim actuator functions like real life (moving the neutral position of the stick). With that option checked you can hold your FFB stick in a fixed position and run the trim without causing the elevators to move. Force on the stick will increase the farther away the stick gets from the trim position, and as soon as you release the stick it will move to the new trim/neutral position. When using a spring stick or not using the special option, the trim offsets the elevator position from 0. This method works for spring sticks that cannot move their trim position but doesn't work well for FFB since FFB can actually mimic real trim actuator operation.
FFB operation is way closer to real life than spring sticks. It sucks that there really aren't many good FFB options on the market, I use a VKB stick for most things since my MS Sidewinder 2 doesn't have enough buttons.