I had instance mission "Take out a small Nemesis Army base" from Lt. Col. Flynn (he is located in Cascade Archipelago in Mole Point Charlie). The zone of mission was FBZ before patch, but it was changed to Talos Island after the patch.
Also, calling Lt. Col. Flynn form Talos would give another mission in Talos. While I haven't test it, but I'd assume that mission will be given in any zone you are calling from.
I had instance mission "Take out a small Nemesis Army base" from Lt. Col. Flynn (he is located in Cascade Archipelago in Mole Point Charlie). The zone of mission was FBZ before patch, but it was changed to Talos Island after the patch.
Also, calling Lt. Col. Flynn form Talos would give another mission in Talos. While I haven't test it, but I'd assume that mission will be given in any zone you are calling from.