I think, and I could be wrong, that this is what happened:
* The Marika we have been following was originally from the Yuri world.
* She was involved in the experiments in the past and swapped places with the Normal world Marika.
* As they got older, both felt out of place, and the Normal world Marika (living in the Yuri world) researched and found a way to swap back.
* Then the story we just read took place.
This explains why both Marikas felt out of place, because they were in the wrong worlds. Now they're both back where they belong. Also both seem to have found happiness, Yuri-Marika with Lily, and Normal-Marika with the boyfriend.