^MQM has a very favourable opinion among shias and its because of large shia population that they got votes.
In that case, all Punjabi and Sindhi shias should be the supporters of MQM, but we know they don't support MQM. MQM has support of majority of people of urban Sindh, regardless of their sects.
Actually MQM got votes there because people in Gilgit/Baltistan saw MQM's work in Sindh, especially Karachi. People there want to see development like Karachi.
It could also be because Giligitis don't like terrorist kharijis, and since MQM is one of very few parties who actively and vehemently oppose terrorists in every way, the people of Gilgit/Baltistan are siding with MQM.
Everyone who criticizes MQM for being an ethnic party should actually welcome MQM's entry in other parts of the country. This may hopefully make it a mainstream political party instead of being just a regional party.
Also, it is not necessary that MQM be able to keep the votes it got. It all depends on MQM's performance there. If MQM repeats there 90s history of Sindh then it will certainly lose their new found support in Gilgit/Baltistan.