That the Albanian form of the name is a little different seems to have no significance, any more than "Roma" being called "Rome" by English speakers. Maybe Albanian Muslims changed the last letter to "a" to make it more Albanian? Or maybe it is to honor Ali the nephew of Muhammad? How will they change names like Pristina, Mitrovica, Prizren, Gracanica, etc?
About 30% of Albanians are Christian, and many of the Muslim Albanians are probably Muslim in name only after decades of atheistic indoctrination (under the Hoxha and Tito regimes). Mother Teresa was an ethnic Albanian born in Macedonia. Some Albanians fled to Italy at the time of the Turkish conquest, and their descendants still speak Albanian...I don't think any of them are Muslims.
Modern Albanian is usually thought to be descended from the language of the ancient Illyrians in the same region...I doubt that the fact that many Albanians adopted Islam under Turkish rule affected the endings of names.
There are already Albanian versions of the names in Kosovo...Prishtina for Pristina, etc.