It can't. Washington DC's population isn't that too great but Mogadishu has 3.5 million which will be 4 million soon. That would me 4% - 5% don't have a federal MPs or Senators representing them in the federal Parliament.
The best option would take German way of federalism. Turn the capital into federal city-state. But on condition that government institution, building, Members of Parliament and Presidency's residency would not have to abide by State laws instead it be under federal laws.
This applies to other government institutions and properties. For example, military bases scattered around Somalia do not have to abide to state laws and regulation eg land ownership. That state's authority like ministers and police do not hold authority there nor can they enter it with FGS permission.
Simply put it, Federal government properties and institution are immune to state laws and regulation while being under authority of the FGS's laws and regulations. While the Capital would become more of a symbolic idea then an actual function.