Will the data protection feature also protect the sqlite file behind the scenes of Core Data?

According to the documentation the answer is YES, sqlite file for Core Data is protected by default:

For apps built for iOS 5.0 or later, persistent stores now store data in an encrypted format on disk by default. The default protection level prevents access to data until the user unlocks the device for the first time. You can change the protection level to assign a custom value to the NSPersistentStoreFileProtectionKey when configuring persistent stores.