Why MQM got so many votes in G-B? One possible angle is the large Ismaili community in G-B.
I think, and correct me if I am wrong, the Ismaili community votes for MQM (for whatever reason) and could have played a big role in persuading their community in G-B to vote for MQM.
MQM won the seat from Skardu-6 which doesn't have presence of Ismaili community. However, the Ismaili community is mostly present in Hunza (Gilgit-6) and Ghizer (Yasin area) which were won by PPP.