No, I don't know how they communicate exactly. However, I imagine between the processor and flash memory proper there sits a flash memory controller (provided by the flash memory manufacturer) that speaks some protocol akin to ATA. That way manufacturers would be able to replace flash memory A by flash memory B with relative ease, because the abstraction of the protocol allows them to ignore how that specific flash memory is implemented exactly.
Is that wrong? Does the OS on smartphones generally have direct access to the flash memory proper?
Edit: I remembered another protocol that I would guess is used in smartphones for communication with the flash memory, namely UFS (which is also utilized with SD cards).
Edit 2: Note that it is irrelevant whether the protocol used is ATA, UFS, or something different.