Theory time!
Gensokyo doesn't actually exist in Maribel's timeline. She's just dreaming of some place that her mind came up with. The only reason why she has things like the cookie from 'Sakuya' is all because she was bending the boundary of dreams and reality.
She and the moonbitches are probably the only characters with actual powers in her timeline as it could very well be that youkai were yet another one of Maribel's inventions.
Maribel later becomes Yukari and decides to go back in time and create Gensokyo based off of her dreams. This exists in it's own separate timeline.
This can be used in order to deny various paradoxes and inconsistencies