Spoiler and a theory
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I think that the ferry sank, and June is the only one that had the ability to survive. The "Follow" ending probably shows that she gave up, the other one seems to indicate that she kept fighting and managed to survive. What I think supports this theory, is the beach being empty and sunny when she's back to the shore, whereas before she sees Roy for the last time, it's full of clothes and, well, the weather.
I ain't no MatPat, but this was fun to think about.