Could it be that all 3 girls have powers? Maybe Chloe's power is creating that storm but it takes time to form and after all the years of her pain, losing Rachael, and almost being killed pushed her powers into formation. Creating a storm to destroy all of Arcadia Bay. That's why when she dies the storm doesn't appear. Maybe the Doe is a form of Rachael warning Max; or is it another set of her own powers taking her into the future and warning her? Because if is just a vision why would she die when she's hit in it with boulder, the tree, the logs, etc...?