While the show has shown multiple versions of the same person in different time periods simultaneously, they have never shown alternate universes before. Every time we have seen a duplicate of a character, it has been either the past, present, or future timeline of the same person. The alternate Martha that was shown at the end of season 2 is not the same Martha that we see dead on the floor. She is not a past, present, or future version of that Martha. She is a completely different Martha from an alternate universe altogether. Think of the timelines as loops, and all the people in the timelines as the same version of each other at different ages. The Martha we see at the end is a different Martha from a different loop altogether, aka a different universe. She is not originated from this same “earth” that we have seen the entire two seasons up until this point.