Teaching hitters how to work a count isn't necessarily about garnering walks, but getting young hitters not to chase pitches they will either miss or have low velocity/low BABIP. Getting ahead in counts increases the number of "hittable" pitches they see. And teaching them not to pull outside pitches, especially outside breaking pitches, is another thing they've been working on, and it's starting to pay dividends, see Alfaro.
Eventually I think this will pay off at every level of the system, but it may take a couple years to break ingrained habits - Franco is a good example, we'll see if they can finally reach him or if the last month was a fluke.
One reason I'm patient this year is I can see progress everywhere, from the majors to the minors - a lot of it is incremental as players rework swings and approaches to hitting and pitching, but you really get the feeling that the organization is finally in the 21st century. They got a story and they're sticking to it.