I was there last week and it did close earlier than the park. I believe it was listed as closing at 6:45 when the park closed at 8:00. A lot of things closed at 6:45, I believe because they needed to get the animals inside. On the train to planet watch they mentioned that every night the animals are brought inside to the buildings you can see on the train ride out there, and it takes up to 3 hours to get them all inside.
I would imagine it closes at the same time as the Safari because on the way out on the train, you go by some of the enclosures where some of the animals spend the night. It would be confusing for an animal to get their signal to come in for the night and be almost to the building and then have a train going by with a Cast Member talking to the guests on the train.
It does close earlier than the rest of the park, and often earlier than the other animal attractions. The last two weeks, when the park was open till 8, it closed at 6. All other animal attractions (Safari, Pangani, Maharajah) all closed at 6:45. Towards the end of this week, animal attractions are moving to a 7 pm close, but Rafiki's is staying at a 6 pm close. I don't know when the closing time will be in June, but it's a safe bet that it will be early.
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