Honestly we can only know for sure once the next game is released. However we can reasonably assume that certain endings such as that of Baraka, Sheeva etc that contradicts with the Mk9 storymode will not be true. Then there are others such as Ermac's, Johnny Cage's endings which can happen since they do not clash with the storymode.
All in all we got to wait till the next game to find out.