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There are not multiple runs.  They way it is setup is you unlock the girls and then choose who you want to end the game with, which save for a single render is virtually identical between all girls so you effectively see all endings even if you just see one.

I hope this is polished later on in the future.

In the page says that there are 16 girls to interact with, I still miss a couple. 

Depends on how you play.  Some girls won't be available if you didn't find them.  Which ones are you missing?