There's a whole lot of excellent Communist Yugoslavian education in between.

I simply don't believe that 40-50 years (~2 generations) of "excellent" (that is questionable description) education can replace centuries of scholarly tradition. We can clearly see that previously Ottoman-owned territories still stand out clearly more than 50 years after independence, indicating the presence of strong societal inertia (which makes sense -- changing people's minds and culture is inherently a slow process that spans generations).

You can't even know if the map is accurate, really.

Considering printing was banned throughout the Ottoman Empire, I very much doubt that literacy levels there were anywhere close to these in Austria-Hungary. The map seems to support this assumption.

Also, it seems like it has more to do with urbanization than anything else.

I wouldn't want to venture into any wild assumptions about the direction of causality here. It could very well be that literacy promotes urbanisation, or that both are dependent on a third hidden variable...