Yah know it's entirely possible Shanks and Nega-Shanks are one in the same.
Given he appeared using a summoning circle, Shanks could easily have a circle hidden in his captains quarters that he uses to go places without his crew he may be living a double life
What if Shanks was always a spy for the world government and feeds them information, that's how they always know what the pirates in the new world are up to, it's why Sengoku agreed to stop the war, it's how they knew where and when Roger would be in any paticular island