It looks like they adjusted exactly the right thing. The black "bellows" looking object is a boot over the viscous damper that controls how the foot treadle and HST input linkage returns to center. The other end of the damper is pinned to the frame. By adjusting the nut you pointed out, you control how far the damper is depressed with travel of the foot treadle, and thus how quickly/slowly the damper will "ooze" back to neutral position.
I am in agreement that you don't want it to stop too abruptly. In fact, it will behave differently depending on what gear you're in, so try each range and see how you like it. On the Kubotas I have owned, they stop fairly abruptly when letting off the treadle, but that still takes a foot or two depending on the speed and the gear. If the tractor really did stop instantaneously when running in high gear at top speed and letting off the treadle, you'd likely get thrown out of the seat. So there should be a little bit of transition before stopping.
The problem people have noticed on other
BX25D-1 tractors is that they don't seem to stop at all; in reality, the damper was taking too long to return back to neutral, thus the tractor coasted for what felt like indefinitely. But the damper would have to eventually return to center, otherwise the tractor would never be able to sit still. It just wasn't returning fast enough to be noticeable.
Dampers are generally non-linear, meaning that the return-to-neutral behavior will change disproportionally to the adjustment of motion. It takes trial and error, or previous experience, to adjust them right. Sounds like the tech at your dealership knew what he was doing, especially if he took the time to show it to you.