I'm not that skeptical about the Ottoman federal identity. The Sunni Muslim affiliation to the Ottoman Sultan was real, there was never a major revolt in Albania or in the Arab Lands. If the Empire manages to get some stability, it'll never lose Muslim support. Christian support is trickier, but IIRC there's an old map in the forum based on the Ottoman census showing how Muslims made up at least 30% of all Balkan provinces.
IF the Empire manages to industrialize alongside Western Europe the Balkans would be obvious center of the most important industries, Muslims from all over the Empire and outside (Circassians) would naturally flow into the Balkan cities and we can expect a Muslim plurality in every important city of the Empire.
Also, as said before, if the avoid Greek Independence and get a more stable and inclusive Ottoman Empire, the Greeks will probably gradualy accept to become a part of the Ottoman continuum, as they actually were - there was no area with a significant Greek population without a Turkish one and vice-versa.