Whenever you're typing something that notification will appear on the notification bar (but it shouldn't pop-up across the screen, it should only be something that you see if you pull down the notification bar). That's just how Android works now (it's been like that since KitKat, I believe). Even if you select SwiftKey as your default keyboard, you will get the option to switch input methods from the notification bar every time you're typing (selecting the default keyboard only means that's the one that will pop up immediately after you start typing).
Only way to get rid of that notification is to have just one keyboard installed. And since you use SwiftKey and the stock keyboard cannot be uninstalled, well...