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Since the hook implementation was added in http://cgit.drupalcode.org/field_permissions/commit/?id=7823ec0 field collections inside an entity with a UID work. If the field collection's host doesn't have a UID though it should check to see if the host is a field collection and if it is it should return the result of running the hook on the host. That should allow it to work for field collections nested to any depth.
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