I think the writers realized there was merit is just accepting there's yet another alt-timeline and I for one think the show is better for it, than trying to rationalize away all the continuity issues with Rascally Roy Thomas-levels of mental gymnastics.
They acknowledged in that episode that Khan Noonien Singh’s activity was supposed to have happened in the 1990s in the original timeline but was happening over 30 years late. So of course there are alterations to the timeline.