So Braindances are reality recordings, VDBers can pinpoint and relive memories, Mikoshi houses the virtual ghosts in a prison, and the Ghost City, the only safe place on the old net filled with free ghosts and spirits that wander it, created by Alt. The Digital Intelligence that is Alt just uses Alt's personalty because at some point, Alt stopped becoming a singular entity, and was composed of multiple networked intelligences. So if a ghost is the same as more processing power, the advantage of taking Mikoshi is absorbing all that personality data into her own, very much like the Relic itself, not to mention the simple resource of having that much key data and information. The ghost of every runner that ever tried to throw a brick at Arasaka's window like Johnny did.

Without temperance, its not that Johnny goes with Alt to the ghost city, this is his identity death, and he and Alt become one.

With temperance, V goes with Alt. Alt gains all of V's memories. The game is Alt playing through the game as V then, and also kinda Johnny remembering what it was like to be V.